The Navy does issue the M11 (Sig P228) to some of its aircrews. Not any particular reason as to who gets what they just have them in the rotation.
The M9 is a good pistol, its just they've spent the last 20 years getting the crap abused out of them and havent been serviced or replaced at anywhere near the rate of the M4/16 family. Mags are old as hell, trigger springs are worn out, etc. Its still a handgun and still capable of shooting better than 95% of the operators using it are capable of shooting it.
If your really down to your pistol and trying to pretend that there would be that much of a difference between an M9 or a Glock or any other handgun, your already f*cked. When Im out of ammo for my M4 and down to the last mag of M9 Im not worried about what handgun I was issued. At that point Im thinking about whats the last word I got over my C-Cell was and how much I do not want to be taken prisoner by hadj.