Wanted to update that finally got this resolved. First two suggestions didn’t work but removing all existing installations/versions of Audacity and then installing one of newest alpha builds did the trick. I used DMG version, not sure if .zip verions works as well. Copied my plugins folder that were previously copied to external drive prior to deleting of older versions of Audacity. Once alpha build was installed, rebooted and ran add/remove effects. Rebooted again after that completed and upon relaunch of Audacity all plugins visible in effects menu and are working now.
I can confirm this is resolved when I installed the latest Nightly Audacity 2.1.3 release from DMG:
http://www.audacity.homerow.net/index.php?dir=mac/audacity-nightly-2017.02.04-06.00-31df61f/
Not sure of the stability of this release though.
I noticed the reason for this in another post:
Re: ClipFix Effect is missing [SOLVED]
Permanent link to this post Posted by Gale Andrews » Fri Feb 03, 2017 9:35 amThanks for letting us know. The upcoming Audacity 2.1.3 will be codesigned with an Apple Developer ID and with some other precautions this problem should not happen when launching Audacity. It might still happen when closing project windows.
Thanks for testing. Not all machines are susceptible to this bug. We don’t know exactly why.
To be clear, alpha builds are not releases and are not codesigned. We are close to release and so the current alphas are believed very stable. This will not be the case after 2.1.3 is released and we start developing for 2.1.4.
The latest alphas from the top of the homerow site do have a fix https://github.com/audacity/audacity/commit/a05d039 that aims to prevent the bug occurring when launching Audacity.
2.1.3 when released without alpha designation will be codesigned. The codesigning itself should offer further protection against the bug. Even there, the bug might still occur if you have multiple projects open and close one of them without saving. There may be other related symptoms such as very slow Gatekeeper verification.
Gale
FWIW…
I’ve been tracking a similar problem for a number of years now.
Apple has been building a new authorisation system. The two main goals are a better system for Apple Pay and one centralised logon for the different stores, the Apple developers site, the cloud and a number of other services, only available to Apple service providers and resellers.
AFAICT, the problem seems to surface on two kinds of machines: 2ndhand and upgraded machines. I’m pretty certain that the problem with 2ndhand machines is related to some keys not being erased, because they belong to the previous owner. And that seems to confuse some security system in OSX.
Why this also seems to happen to machines that underwent an update from one major version to the next, I don’t know.
It is all just info cobbled together, as there is NO official documentation from Apple. Security through obscurity has always been there.
I know some keys (or parts) are stored on the SMC. That’s how it happens with machines that were sold without harddisk. It’s also why you can’t steal keys or bypass disk encryption by simply putting the harddisk in another Mac. Even desoldering and transplanting the SMC won’t help, as some numbers get calculated from serial number (which you still could transplant) and a number of other, mainboard related numbers. The point is that the key system is also used by Gatekeeper. I only wish I knew how.
It’s known in the repair community that the SMC’s memory suffers from memory-loss in certain cases, resulting in a machine that won’t boot. My query started with one of my MB Pro’s SMC going bad. When I put the harddisk from that machine into an exact same machine, everything worked as expected, except my Apple dev account. And recovering the password by mail, or doing a clean install didn’t help. It wasn’t resolved until I did a clean install on a third machine that it got resolved.
I suspect Apple knows about these problems and that’s one reason why they will replace the SMC with a “Secure Enclave” ARM processor in future builds. The newest MB Pro’s with TouchBar already have these, but they also still have the SMC, for backwards compatibility.
Reports about this are on the net. Usually under the moniker “Why can’t I logon into my Apple dev account?” Of course, not all of these are related to the key problem. Humans do error sometimes too 
In 2.1.3-alpha before the code fix I quoted above, I got the bug on Audacity launch very frequently. All plugins not shipped with Audacity disappear from the menus, and LAME and FFmpeg can’t be accessed. My machine was bought new (a mid 2011 Mac Mini). Partitions that have been upgraded from earlier macOS and those having a fresh Sierra 10.12.1 or later install were equally affected.
The most likely explanation for the problems seems to be timing problems that mean things that should happen do so too slowly then as a result Gatekeeper no longer trusts Audacity.
Gale
Still sounds like a problem with keys to me…
But it’s good to know it also seems to happen with factory supplied OSX installations. I’ve never trusted those 
For the record, I’ve owned this machine since new (Late-2013 MBP). Of course it’s been through many major OS updates though.
Hi,
I used Audacity yesterday… everything worked well.
Today: want to use it again… the “missing Nyquist files” message pops up.
I am using Audacity 2.0.3 on Mac OS X Yosemite 10.10.5
It worked well yesterday…
Are you sure that you are using the installed version, and not running Audacity from the downloaded (not installed) DMG file? Running Audacity from the DMG will give that error.
Audacity 2.0.3 is pretty ancient. The current version (for OS X 10.6 and later) is Audacity 2.2.2, which you can get here: Audacity ® | Download for Mac OS
Thanks a lot guys! For me the shell programming worked! 
Are you aware that you are replying to a topic that is over a year old and relates to a different operating system to that which you use?
Other than that, what does your reply mean? This topic is not about shell programming.
The guy who had an idea for fixing told me to run the audacity shell. Also, I do have the same problem on the device I am using this. But I have another problem now… As soon as I use one effect, all the effects turn grey. Also, a nyquvist code I tried to use did not work. Would be very happy about ideas
Which guy?
Fixing what?
What does “run the audacity shell” mean?
The same problem as what?
What device are you using?
What operating system are you using?
Which version of Audacity are you using?
I meant this guy. No idea what it means, I am completely technologically inept. I use audacity 2.1.0, macOS Mojave, version 10.14.3
Thank you for your time
Kilian
He passed away in 2017, but he had a name: Gale Andrews.
That’s a really old version. The current version is 2.3.1, and it is available via the Audacity website: Audacity ® | Download for Mac OS
Your profile information says “Operating System: Windows 10”. Would you like me to correct that for you?
Well… I use it from both devices, but on the windows 10 one I have had problems with the mic. Sorry to hear about his death, and thanks for the advice. I am going to update my audacity. Btw, I appreciate all the work you have done here a lot, and in a week or so Ill have a more exact question, I need for building an app (as you might have already guessed by my username ;))
hu…l. With the new version of audacity everything seems o work more or less, but now the entire buttons from the toolbar, like play and stop/record are on a random part of the screen. Sorry if there is already a thread on the topic, can’t find it tbh.
Kilian
Try resetting the toolbars (“Tools menu > Toolbars > Reset Toolbars”)