@corruptedevil: Err, no, sorry, you've got it backwards.
They very clearly talk about ZEKE being "complete" in the briefing tapes of Ground Zeroes. About waterproofing ZEKE and the nuke, about an underwater test and about a 300 foot seabed test. Because they need to hide their nuke and Metal Gear for the IAEA inspection, should be the first couple of minutes in this video:
And in Peace Walker, they show Paz falling out of ZEKE, falling into the water - there's no implication that ZEKE also ended up in the water.
Starting at 29:35, running 'till the credits start, or so.
Anyway. As I remember from Peace Walker (where Fulton recovery featured), Fulton "ammo" was limited, but capacity could be upgraded through research, up to 13, I believe. In PW there was a special item to analyze soldiers before you Fulton recovered them - something like that might appear here as well.
edit: Meh, video embedding seems to be a bit funky today. I'll settle for links.