Although I don't have an agent, I'll tell you what I know of friends who do have agents. They have negotiated that all epub contracts go through the author and not the agent. One reason is that for a lot of agents, the pay out from an epub isn't high enough.
Additionally, the NY contract typically deals with a mess of rights the author shouldn't negotiate on their own while epubs typically want just digital rights (that varies, of course). Succinctly put, NY contracts are trickier waters to navigate than epub contracts.