It may help to reorganize these in “domains” (not Xen domains). For example, the use of work-mail, work-documents and such. In order words, one may think of qube names as [group]-[name]. That way they will be neatly organized.
DispVMs taking too long
if you don’t mind the risk of some open documents being able to see other open documents, then we have a recent thread discussing a possible solution to this:
Divided UI for managing qubes
I actually haven’t actually experienced this. For 90% of my actions I only need the Qube Domains widget (and some i3 shortcuts)