Ok fixed it. I just went into dev menu on my theme pack file. Saw the file id and went back to the installed programs on the devmenu, found the program with the same file id and deleted it. After this the pack installed fine. From what I understand every time I go into eshop I will have to install the theme pack again? Is that right?
I have my games in 3ds and 3dz files so I won't have problems like those. The only cia that I have installed are the themes biblue menu and coin setter. Any update that I need for anygame can be installed genuinely from the eshop so there is no issue with them.