The 256 (hex FF) mod limit is one of 2 limits you may run into with mods - the other one is the total number of mods, activated or not, in your data folder. It seems that the game looks at all of the mods in the data folder on starting, and decides whether to load them or not. If the total reaches a particular number somewhere over 400 it will crash. The easiest way to deal with this is to move any unused mods out of the data folder. Or, if you use Wrye Bash, activate the ghosting feature which hides unused mods from the game.
Both of these are hard wired into the game engine and cannot be changed - The storage space allocated for addressing mods is set at one hexadecimal byte (FF) which is either 255 or 256 depending on how you deal with zero. A byte is the smallest usable chunk of memory in a computer. The next value up from FF would be 2 bytes which would give us hex FF FF or 65,535 which would have given us far more space for mods than we could possibly use. And tie up a chunk of space in memory that would be mostly empty. Personally I think 256 should be sufficient. Try removing some of the mods you aren't really using to free up some space if you can't merge them.