Finally, 2 MAJOR bugs are solved!https://github.com/rdanbrook/nestopia/issues/46
I've talked with Marty and he helped a lot:
Sound decyncs caused by autodetect samplerate subroutine.
Bug is gone after disabling that part of code.
Thanks to FHorse (puNES Developer), he fixed dendy mode inaccuracy caused by Vblank and NMI flag were set prior of sleep scanlines (in the part of the code added since 1.38).