Im talking about putting all the simple mods which have just a single data files folder with a single .esp file.. can I put them all into a single data files folder to minimise clutter in my mods folder?

I'm not 100% sure I understand what the question is asking, because it seems like you're asking if you can put all of your mods in the same folder.

The game is looking for a specific path.... Morrowind/Data Files
If you add in Morrowind/Data Files/My New Folder the game will not be able to find the esp.

Besides, all your mods already are in one file.