I have the same issue - I first noticed it in Hatari, the ST emulator, then on the Amiga emulator. I added a section to my Hatari setup guide specifically mentioning it.
I experimented with a wireless Logitech mouse, a wireless Microsoft mouse, and a wired Microsoft mouse (all laser type units).
It seemed to me that even on the Raspbian desktop the mouse tracking isn't smooth - I couldn't get a genuinely straight line even if moving any of the mice along a straight edge such as a ruler.
The effect is relatively subtle on the desktop, but it seems the lower resolution of the ST / Amiga emulators is amplifying the issue.
I spent a while messing with low-level settings to alter mouse input acceleration and so forth, but never resolved the issue.