Could you please explain better this one " does not show what other packages have dependencies to the package you're about to delete "
Let's make an example, shall we?
You see a look called "Anna" which you like, you download it (let's call it "packageA.var") and put it into your AddonPackages directory. If you try to load the look "Anna", you get an error telling you it uses a skin from another package which you then also download (this will be "packageB.var") and add it to your AddonPackages directory as well. You then realize, the creator of "packageB.var" included a look as well (which features the skin from this same package), and this look is called "Barbie" (with no further dependencies).
So now you'll have two new looks, "Anna" and "Barbie", although you only wanted to have "Anna". Currently you can load both those looks without any errors.
If you now now open the AddOn-Manager in VaM and scroll through the installed packages with the intend to "clean up" some packages, you might stumble across "packageB.var" which contains the "Barbie" look -- and because you don't like this look, you want to delete it. But because the AddOn-Manager does not show you something like "Hey, remember: the "Anna" look also needs the skin included in this package", you will break your "Anna" look if you just delete packageB.var. So once you've deleted "packageB.var" through the AddOn-Manager, your "Anna" look is broken again, and you will have to re-download "packageB.var" if you want to get it fixed.
Here's how I deal with this:
First and foremost: I only install a single look/scene/clothing item at a time with all its dependencies, then check the newly installed look/scene/clothes to see if they're working as intended. If some (or all) of the additional packages I had to install contain more looks/scenes etc., I'll ask myself: is this one single look/scene/cloth worth keeping all the other stuff? If not, then I'll delete all the new files again. Otherwise I'll keep them, and move all those packages in a subdirectory of "AddonPackages" called something like "keep" (any name will do). If those additional packages come with their own "scenes" for example, which I don't want/like, I will just "hide" them in my VaM browser.
That's the most basic way to keep your VaM installation tidy and clean.
Once in a while I do want to clean up stuff, but instead of using the ingame AddOn-Manager, I manually do move those Packages I intend to delete from "AddonPackages" to a temporary directory outside of VaM. Then I'll start VaM again to see what packages (aka what looks/scenes/clothes etc.) I've just broken by removing those packages from VaM. Then I'll have to decide again, whether or not I will also delete those now broken packages, or if I need to re-add the missing packages from the temporary directory back into my AddonPackages directory.
Hope this wall of text helps ;-)