Personally, I thought it was pretty easy to see why Maya was reluctant to tell the MC that she still has a girlfriend. By the time Maya trusted the MC enough to get into the whole lesbian thing, she already had strong feelings for him herself.
Beyond just being extremely confusing, this left her in real bind. If she tells him about Josy, the MC can basically react in three ways: he can be angry Maya hid this from him, he can end their proto-romance out of respect for her relationship, or he can stick with it and ask her to break up with Josy.
The first is obviously the one Maya most fears (and not without cause as it turned out, though the circumstances became worse with her indecision). But even the latter two have a high price because either would effectively force Maya to choose between Josy and the MC at a time when she has serious doubts about both: the MC being a boy makes her worry he is just a momentary fling, but Josy has all but abandoned her by this point and what little contact they have had has become toxic.
So it's no wonder Maya kept waiting for some clear indication of which way she should choose before she explained it all to the MC. Sadly, by then it was too late. Happily, a fourth option presented itself in the aftermath (assuming the MC played his cards right).
