If the software was installed with administrator rights, it will act as expected whatever your rights. Most AV stuff refuses to install without admin rights. In general, it needs admin rights anyway to delete stuff during the cure.
A couple of products have had issues from time to time: I think ESET's online scan needed Admin rights but didn't ask for them, and maybe MBAM a while back.
So, almost certainly yes, everything gets scanned.
FOM.