If I install a weapons mod with hundreds of mesh/texture folders then realise I dont like it.. will wrye mash remove all those textures for me?

Also I have a daggerfall books collection mod which is giving me a 'you might experience problems with this game' message in the launcher... How would I go about fixing this using Wrye mash?

Yes. If you used it to install the mod in the first place.

Otherwise, no.

What you can do if your really worried is make a copy of your data files folder before installing the mod, then if Wrye Mash can't remove it for some reason, then you can replace the data files folder with the copy.

If you had already installed it without Wrye Mash, what you can do is go ahead and tell Wrye Mash to install it anyways, THEN tell Wrye Mash to remove it. Poof...textures gone. Alternatively, you could use this little tool http://www.nexusmods.com/skyrim/mods/27718/? by qqqbbb to make yourself a custom uninstall bat file for the mod and do it that way. (Yes, I know it is on Skyrim Nexus, that do not invalidate the use of the tool for this purpose though)

If you look in Mash in the mods tab, it likely has a yellow colored checkbox, go over to the right side of the window, click on any master file in the masters list, drop down to the bottom of the screen and click the save button.

Awesome that seems to have done it thanks.

For some reason, the mod works and the game loads fine... but Im not seeing any of the books in the shops.

This was the mod -

http://mw.modhistory.com/download-11-2443

In the readme it says Both Tribunal and Bloodmoon expansions are required, and may need to be run through the levelled list merger... how do I do this?