Well... Now after reboot middle mouse emulation is enabled again:
xinput list-props 8 (my mouse ID)
libinput Middle Emulation Enabled (291): 1
While the next string from the output says:
libinput Middle Emulation Enabled Default (292): 0
Seems that .xsessionrc doesn't work now and that's a bug, I guess.
But I don't know what package might have caused this issue.