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This might be a very dumb question that could be answered by carefully re-reading dialogue early on in the game, but just to be 100% sure and solidly clarify, given I can't remember if this was cleared up or not, but do guests still have to pay money to stay the night like a normal hotel or are guests allowed to stay for free, given as Asterion did make it clear it was a sanctuary for the lost.

The normal rate was kind of low but they can be free if they want to.

There's only so long staff can work for free even with the most obvious charity.

I thought staff were paid with currency and valuable items the owner could generate using the Labyrinth? 

You CAN'T generate currency.  And yet gems are ALMOST no problem.