There have been people who've modified the cooling on the RB1100AHx2 and CCRs. The problem is that they follow mikrotik's old style of cooling hence the reliable but noisy fans. I bought quiter fans for my CCR before but one of them failed so i just put the stock ones back on. When you have 2x1U deep fans running next to each other in a 1U metal chassis they make a lot of noise.
There was one post on mikrotik forum of someone using a big heatsink in keeping it cool and modding it too. See if you can change the fan profiles in the system -> health section.