I was looking to book a short term rental apartment, and I used an agent that gets a 5% cut. In the process of sending us info about an apartment I was looking at, the agent forwarded a message from the seller that contained pictures and info as well as a message that he’d rather go for a lower price than have the apartment stay empty. Because of this I now have the owners direct email. Can I contact the owner directly to try and get a better price? If so, do I have to give the agent a cut? And would it be a cut of the price we pay or the price the agent wanted?

It is dishonest to contact the owner directly. The owner information you were exposed to was a mistake. Your source of information about this apartment is this agent. If you would contact the owner you'd have to pay the agent the full 5% cut of the price he quoted. It is a perfectly legitimate business to be an agent and negotiate the price with owner and renter.