Themehax requires 9.0-9.2 in order to work and no you shouldn't lose anything if you install 10.1 emunand. just unlink it before updating because theirs a chance of it updating the sysNAND too.
Well it can be run via ninjhax 1.x but it can also be run through the 3ds browser and if you downgrade mset you can also launch it in the system settings