to the best of my knowledge there are no official penalties for not having a working grav deck.
with that said... most of the issues would be health/morale related. and likely the health issues would take some time to kick in.
I know there are a lot of issues but look at 2001 a space odyssey, and more recently "the Martian" the grav decks on battletech craft are not exact matches, but the principles are similar. they include rotating sections that provide "centrifugal force simulations" of gravity, the biggest issue with the Martian is that the hermes spacecraft is too big, and has way too much internal volume to be practical, there are other places where the "science" is flawed or problematic but...
but think about it if the grav deck is primarily for exercise and recreation having it broken, is going to make long term 0g health issue to crop up a lot sooner, but I believe most of the issues still take weeks to months to become issues. Morale on the other hand will start being affected more or less immediately.