@ritualclarityIt predates the virtualization like MO has, everything exists in the data folder. I have a scary amount of stored in NMM and installed currently. Right now my data folder is 175 GB and according to NMM I have 1736 total mods in it, 409 active mods (some are multi-part mods) and 247 active plugins. I still have some older versions stored in NMM of various mods in case I have to roll back for some reason. I am a bit of a mod packrat.
I have had little issue with NMM from the start and have only had to reinstall my mods from nothing twice, once was an issue with an older version of NMM that screwed up the entire mod installation and once due to an unexpected HDD failure. My current install was done mid November of 2014 (14th through 17th) and have been going fine ever since. As it is I rarely update some of my older mods unless something else requires it, unless the new version fixes problems or has features I really want I don't see the need so long as it works.
I do use Wrye Bash but mainly for the tools in it and info it provides at a glance.