The most dangerous thing for me is, if you are creating looks with morphs from different Var. Hoir or clothes would be the similar, but not that much dangerous.
Once you delete some Var, your own characters won't look the same anymore, and it is hard to find the single Var with the missing morph. This will put my own carefully done creations into danger!
For my best looks, I therefore use "Morph Merger", to merge all used morphs for a look into a single one (or better - two, for head and body). Though, this makes it hard to change the look afterwards.
The second thing is the way Vars are using other Vars as dependencies (which will have their own dependencies, too), even if they only will need a small part of it.
I have a nasty error message asking for a dependency with a "Lamborghini", for instance.
I am sure, I never ever have downloaded a scene with a sports car in it!
If you don't have many scenes and/or Var files, you could move away a certain ammount of Var, start your favourite scenes one after another, and have a look at the error messages, aso. Though, this is very cumbersom... and nearly impossible, if you have hundreds of them.
The questioned tool should be able to handle at least those two big issues... Maybe it is too complicated.
The Var system for sharing stuff is way better than what we had before... but, I doubt it was ever tested with hundreds of files and user created scenes before rollout. Unfortunately, I don't have a better solution.