You could certainly do that. I think UK Germany makes a housing for the Canon 550EX flash. In this case though, I believe you need special bulkheads on whatever housing you use. I'm pretty sure someone, maybe Alex, has the Nikon version of this, but I'm not sure anyone here has tried the Canon version. It's certainly worth a shot, although it's a bit more expensive than a good dedicated UW strobe. If I remember correctly, the UK Germany housing for the 550EX was about $350, the 550EX itself is about $320, and then you have to factor in getting the correct bulkheads put into a housing.
Truth is, if you get a strobe with a manual controller to adjust the amount of output from the strobe, like the Ikelite DS-125, you won't miss TTL too much. At least that's what everyone who doesn't have TTL seems to want to believe (myself included). 
Regarding the dedicated strobe housings for both E-TTL (Canon) and D-TTL (Nikon), Seacam makes housings for both manufacturer's speedlights. I know Subal does for the Nikon speedlights as well, but don't know about whether they offer a Canon speedlight housing. In the Seacam line, these strobe housings are called a "Systemflash".
Over the years we have sold plenty of Systemflashes to shooters who migrated from film and figured they needed TTL on their digital systems. No special bulkheads are required as they operate with the standard Nikonos 5-pin connectors. They do work well for fish and macro, although I think most amphibious strobes tend to be more ergonomic underwater.
However, the beam angle is not really sufficient for wide angle, and since TTL is a marginal technology for wide angle subjects anyway, the housed topside strobe is not a great choice for wide coverage.
So, that leaves shooters using the Systemflash for fish and macro, and a submersible strobe for wide angle. So long as you really want TTL and don't mind traveling with duplicate systems, that's OK. Of course the Fuji S2 offers the best of both worlds ... TTL with conventional submersible strobes. With the immediate review from the LCD we find fewer shooters depending on TTL like they used to, and embracing submersible strobes for all their shooting.