My ears tell me that they are identical.
That’s not surprising since “CD quality” (16-bit/44.1kHz) is better than human hearing. 
Often a good-quality MP3 (lossy compression) can sound identical to the original (in a proper blind listening test).
And my eyes too because in Audacity, the wave form and the spectogram are 100% identical
The waveform doesn’t have enough visual resolution to show even 16-bits and I doubt the spectrogram does either. The spectrogram sometimes shows a difference at higher/lower sample rates (96kHz vs 44.1kHz) and often the spectrogram will show a difference with MP3, but that doesn’t mean you can hear the difference.
Does that mean the file presented as 24bits is just a 16bit that has been “upscaled”?
Is there a way to check that? How?
It’s not always easy… I found a plug-in called [u]Bitter[/u] that’s supposed to that. If you Google, you can probably find similar tools.
If it was “simply” upscaled the 8 least-significant bits will be zero and that would be easy to test. Those zeros take just as much space in an uncompressed file so the bitrate is the same for a “fake” or real 24-bit WAV file. A bunch of zeros are easy to compress so the FLAC would be the same size (and bitrate) as the 16-bit file.
But, simply changing the volume by 0.1dB, or dithering, or changing the sample rate, or almost any slight-effect will fill all of the bits with data. It wouldn’t be hard to “fake it”.
I tried an MP3 (ripped/converted from a CD) and Bitter shows it as 32-bits which is “mathematically true” but meaningless in terms of audio quality/resolution so it’s not hard to fake-out Bitter.
Should I delete the 24bits “useless” file that takes twice the space on my hard drive?
You already said you can’t hear a difference so that’s probably an “emotional” decision. If you are doing any editing processing there might be an advantage leaving at the highest resolution.
I have been told that most of the so-called 24 bits sold on the digital market are “fake” 24 bits, and only upscaled 16 bits.
Probably not “most” if you’re buying from legitimate suppliers. The pro studio standard is 24-bits/96kHz so they certainly can distribute 24-bit files. And, some people share true-24-bit “vinyl rips” even though vinyl is not as good as CD.