If large military helos are regularly (interesting to know how often this happens) operating below 1000' over built up areas, they are breaking our rules unless following ATC instructions. In that case, report them to Odiham/Benson and you should either find out why (if there were any mitigating circumstances) or stop them doing it again.
There is always a temptation to sightsee but 1 o'clock in the morning really isn't appropriate - if this is what they are up to (and I suspect it is an isolated case) then I apologise for their lack of consideration and professionalism.
The Chinook may be noisy but it is an awesomely capable helicopter which is why we use it.