However as the load order is setup via a text document, any program that interacts with said document could disable mods, and also modify the load order. The game would straight up crash if a mod required another mod that was not present, so that Could potentially be the only other time that mods would be automatically disabled, however that is not the case and said mods would not be disabled automatically. Note: ESL files can still add onto that limit, if the mod manager does not support ESL files, and as such classes them as part of the hard limit of ESP/ESM files.
Typically the only time mods would be automatically disabled, is if you exceeded the 254 ESP/ESM mod limit, mod managers would disable any additional mod that exceeded said limit, however it might also be possible that the game may also disable additional mods that exceeded said limit, every ESP that exceeded that limit would be automatically disabled.