You can think of IOS and cIOS numbers as slots (as in placeholders). By installing a cIOS, you put some code in it. Then, you tell your USB loader which 'slot' to load the game. Hermes's cIOS typically take up slots 222, 223 and/or 224 while Waninkoko's cIOS is typically installed in 249/250 (and the most recent versions in pretty much any slot, if I read things correctly). As such, you don't usually have to make a choice, as you can just install a bunch of cIOS'es and tell certain games to use certain cIOS'es.
Now...since you wrote "reinstalling", I assume you're asking whether Hermes's version 4 has an advantage over version 5. And since Monster Hunter tri needs IOS 37, I assume you want to install v4 as a merge of 38 and 37.
Now...that is one way to get MHT to work. And it won't break compatibility with other wii games that I know of. However, that very cIOS won't work with the DLC of music games. And if you want to use uloader to play wiiware/VLC, then you should also use v5 (with a base IOS of 37).