We have several webshops, all partly using the same Custom CSS (about 1800 out of 1900 lines in total). The others 100 lines are bascily shop-specific LESS values for colours, and images and such. Can we somehow make a «master.less» file and integrate that in «shop1.less» «shop2.less» «shop3.less» and so on..?

Why not?

For example, in the design/themes/responsive/templates/addons/my_changes/hooks/index/scripts.post.tpl hook try the following code

{style src="addons/my_changes/master.less"}
{style src="addons/my_changes/shop`$runtime.company_id`.less"}

(!) Not tested