It's heavily implied that they are spending time together doing things that isn't directly shown, though certainly more limited than they would like. The game is from MC's point of view primarily, so unless there's a narrative reason to show it, the dev isn't going to show every scene where Josy and Maya do stuff together without you.
Maya and Josy's relationship does have problems, but personally I think they'll be able to make progress on their issues once the loan issue is solved and they can be more open/public. Having to hide something like that can be a huge burden on a relationship for a myriad of reasons, including limiting the time they are able to spend together and introducing doubt of if their relationship has a future (due to the external pressure itself).
As for their feelings being imbalanced, that's also frankly realistic in poly relationships. A relationship of 3+ people where everyone likes everyone evenly pretty much doesn't exist. While that certainly can lead to problems if people have unfulfilled relationship needs or expectations, if people are still having their needs met (the extent of which varies from person to person) and communicate if they aren't, it can be perfectly healthy to have stronger feelings for one person in a polycule. That said, I don't know how much DPC is modeling the triad on actual poly relationship dynamics, so any real life correlations should be taken with a grain of salt.
Taken from a game-design and narrative point of view though, I think having the throuple fall apart regardless of what you do would be a very bad decision. It would remove agency from a medium where your choices generally are supposed to matter. The same however also could be said for having the throuple survive regardless of your choices. That's why I personally think that there will be paths to both outcomes.