The MDS can support jumbo frames, so if you can have the link configured to handle 2300 byte frames that would be the best option and provide the best performance for FCIP. The MDS uses PMTU discovery, so if the MDS ports are configure for 1500 bytes, it will not send frames larger than that. It also sets the DNF (do not frag) bit and if it gets back ICMP message that frag was needed but not allowed, it will build a smaller frame. The goal is to build 2 IP frames for 1 full size FC frame in the MDS, not let the network do the fragmentation. That said, even if the MDS is taking a 2000 FC frame and creating a 155 and a 500 frame, the other MDS has to re-assemble the FC frame and that will impact performance somewhat. I think the actual math for the largest IP frame is 2282, but 2300 seems like an easy number to remember.
The MDS does not bundle frames, so if the application is generating 1000 byte frames, FCIP will send 1000 byte TCP frames (plus headers)
If compression is enabled on the FCIP link, then the MDS will compress the FC frames, and you might have multiple FC frames in a single TCP frame.
Hope this helps,