I had the same issues only recently (june 2021)
Here is what was happening:
When Audacity 3.0 or 3.0.2 used (on Win10 or win7 same result) and my project had many (60 up) parts labeled and marked, it started lagging to any click, even deleting a simple track marker line would take first a minute to respond and the time would increase with every new click.
25 minute audio would take up to 20 min to save and close.
What I did is export the audio to mp3 file.
I re installed Audacity 2.4 and imported this file. I put back all the markings and labels to this and saved it. It works like a charm. No lag nothing.
Now I have also imported this mp3 file to Audacity 3.0 and works fine. I have done all the markings and labels and works fine. The original .au3 project had a lot of edits like volume changes, deletions, insertions, but lagging started to apear when clip fix was used once or twice.
What I observed is that 2.4 uses a different method to save the edits, has lots of subfolders associated with each project and projects have .aup extension where 3.0 has only 3 files associated with each project with .au3 extension. Older version projects are not compatible with new Audacity.
I hope this will help