I have 3 non-evil PCs that are going to run avernus soon and i was wondering if bags of holding would cancel out the disadvantage to checks and rolls due to the fact that inside is a different pocket dimension.

Personally, I would say no it wouldn't, because the fact that you have the soul coins and are carrying them around is going to sit on the conscience of the characters - just because they are in a bag of holding doesn't mean that you don't have them/can remove them from your mind, so I would say its reasonable for the disadvantage on checks to still be there. But once again, that's just the opinion of a frog who sits at the bottom of his well, and D&D can be played however you want it, so find what works best with your group and use that - if they think that they shouldn't have disadvantage and most of the group agrees on it, then sure, write the disadvantage off by, for example, saying that they forget the coins in the heat of the moment, or something similar.

Hope your campaign runs smoothly!