Changing a module with a theme

[Lpeek]

I'm just wondering if there is a way to change a module without the possibility of breaking it in a future update? I can obviously update basic css in the themes directory but to make any proper changes (layout, text etc) it needs to be done in the modules directory.

 

Will this not cause problems when there is a prestashop update? I don't want to have to completely re-theme all the shops modules every time I update.

 

Is the only way to do the very 'hacky' css changes? so I would hide/display certain html tags in the block through the css theme file? That also doesn't seem like a very clever idea?