The MP5SD3 is a common carry SMG for spec ops units. During my time your options for a suppressed weapon fgor use during "Quiet time" was the MP5SD and the PPK/S in .22LR! So the MP5 is a natural. It is quiet as a whisper, it is ACCURATE as hell, controllable fire, and efficient. It is also a pain in the ass to keep clean and in firing condition once it has been in the field for 6 weeks straight without the oppotunity for a detail cleaning.
a 9mm Subgun makes a good bushgun believe it or not. You won't engage at 300M in triple canopy, with the MP5 system you can carry at high port and engage targets by reflex from 5-50M with no problems, and the subsonic Samson rounds aren't "Weinies". For close up work I would take an MP5 over ANY gun on earth, and I am an AR fan. Shyort enough to control and not long enough to be snatched away if you arent paying attention, and accurate enough t put a 3 shot burst within 1/2" at 25'. You just cant beat that.
As far as the M16 Pistol goes.. two ideas (I dont know why it was in the movie). "Clark" the chracter, is a former Navy S.E.A.L. , and they had all manner of custom, chopped weapons, including weapons similar to that one., OR.. (more likely) The prop man thought it looked too cool to leave out of the movie! :)