Some of arabic letters are showing as squares

the ARABIC LETTER VEH (U+06A4) is showing sometimes as a square like here:

I have installed these fonts repositories:

That’s odd. noto-fonts provides the NotoNastaliqUrdu-Regular.ttf file, which should be the one used for the missing glyph (at least, according to opening that page on my system).

Reinstalling noto-fonts might help. Also check if /usr/share/fonts/noto/NotoNastaliqUrdu-Regular.ttf is a file on your system. Finally, are you running any kind of custom font configuration?

the problem was solved by just uninstalling noto-fonts and ttf-ms-fonts, should I reinstall noto-fonts?

Arabic now works fine on Chrome and Firefox.
but on Firefox, Latin in the browser’s UI is thin/small, and the same for some websites.

It sounds like noto-fonts might have been corrupted on your system or similar, so I’d recommend reinstalling it.

In fact, given that Firefox is having issues and you should have a proper Latin font in ttf-dejavu, I’d perhaps go as far as saying that you might want to reinstall all your fonts because it may be that the entire fonts directory has gotten a bit damaged.