Are there any levels on which PAL is the preferred version? Also, if you're running the game in the 50hz mode, does the in game timer also slow down or keep going at the same speed?

The reason I'm asking is that I can play both, and I know that for some of the mario karts the slower framerate can be an advantage.

Got my answer from the discord so I'll post it here in case anyone comes across it.

PAL is generally the same and there's (arguably) no level where NTSC is advantaged, so it doesn't matter all that much.

Play in 60hz as the 50hz mode is just 60hz but with skipped frames. There isn't any time conversion like in MK64.

What do you mean "level"? There are certain modes where one is better than the other (NTSC or PAL).

Marth can wall-tech after being hit by a flipper on his Btt map only on PAL, due to weight difference. He is 87 weight in NTSC and 85 weight in PAL.

PAL can only use "meters" mode in HRC, whereas NTSC can use either "meters" or "feet" mode. There are slight differences between the two, most notably in "feed" mode the platform is a bit smaller.

Marth's down aerial is a diagonally hitting spike in NTSC but a vertically hitting meteor in PAL, allowing him to bat drop in HRC more easily.

Pretty much all differences are documented here: https://www.ssbwiki.com/List_of_regional_version_differences_(SSBM)