Yet another update - the problem persists. It's hard to test because sometimes it takes days for the problem to manifest, so I think I solved it, when in fact I didn't.
I tried deleting the sleep image, resetting the SMC, PRAM, I even wiped my drive and installed a fresh Sierra.
It still happens. Could it be a hardware defect? Not sure how this is possible, because everything else works fine.
My current plan is to try and test without 3rd party apps (for example, turning off BTT before putting it to sleep)
Also, disabling hybernation in the Terminal
I could take it to service however, I don't have Apple Stores in my country, only authorised service providers, and my friend recenltly had quite a bad experience with them (they actually managed to make things worse and were unable to fix a problem, he ended up contacting Apple and after three (!) months of hassle and without a computer, Apple sent him a replacement). I am reluctant to risk being without my computer for months because of this, especially since it only happens in 'deep sleep' and does not affect my work. Still, it's annoying.
I may wait for the next major macOS update and hope it, somehow, fixes itself. Not sure what else to do, really.