I applied to both Pediatrics and Combined Medicine-Pediatrics. For the most part, I was honest and let them know I was applying to both. I didn't want to look bad as if I was trying to be sneaky. Plus, most program directors for these two specialties usually oversee both programs, so they were bound to find out anyway. It never seemed to be an issue. In fact, I think it showed that was I really interested in their school/hospital.
However, this might not be the same if someone were to apply to both FP and OB/GYN, for example. Since peds and med-peds are pretty much similar, most PD's know that applicants applying to med-peds might fall back on categorical peds because there are fewer spots for med-peds around the country. This helps increase your chances.
I'm sure someone else can shed light on this who has been through it and applied to two competely different specialties. I do remember a lot of people advising me in the beginning (I was initially going to go for OB/GYN and Peds) that it's not a good idea to apply to the same hospital. PD's and residents talk and you're bound to get "caught". It may make you seem like your wishy -washy and not serious about one specialty. You could take the chance though, as most PD's may not communicate with eachother.
Initially I applied to UC Irvine for both Peds and OB/GYN and no one noticed. I do remember being terrified on my interview day for Peds that the OB/GYN residents and/or PD would see me and wonder what the heck I was doing! Of course in the end I only ranked Peds so it was never an issue. Perhaps if I had ranked both, word may have leaked out...
I hope this helps, I would talk to residents who may have done the same thing and actually ranked two different specialties. I remember meeting quite a few residents on my rotations who did this and it never seemed to be an issue. The only thing they all said was that they were so scared to get spotted by someone on their respective interview days.
Just my two cents...