As others have stated, the big question is if you plan on keeping it forever, or selling it one day.
Also, as morbid as it may sound, think about the people you leave behind when you visit the great computer museum in the sky (if that's your belief). Will your loved ones be able to sell it? Will they loose lots of money on its sale because you like it to look perfect? Those are things to think about. Remember, most family members don't share our love of retro computers.
That being said, I personally have over 80 computers in my collection. So during the 20+ years I've been collecting, I've developed a few simple rules I follow.
Those rules are:
1) I try to have multiple copies of each computer. One copy for "never touch, leave ugly, never mod" so that IF I decided to sell (or my family does after I kick the bucket), then it should (hopefully) be the most valuable. I then have another copy that I may retro-bright, re-cap, mod, etc. Now, that isn't possible all the time. As much as I would like to have a few more PET's, for example, they are a little expensive so I only have one. Same with my boxed Coleco ADAM. In your case, you only have one (that you mentioned) of the NeXT Cube. So this rule may not apply to you.
2) If the computer is ALREADY altered before I got it, then the damage is already done. For example, I only have one TRS-80 Color Computer 1 that I bought from eBay. The seller painted it white to match the model 2 an 3. So, the damage is already there. I don't feel guilty about stripping that white paint and restoring to silver. Or even adding a composite mod. It's never going to be factory original anyway.
3) If the computer is so damaged that the damage is preventing it from being useful, then I may restore it as best I can. Cracked cases, engraved initials, etc. Again, damage has already been done.
4) If the computer (or component) isn't hard to find, isn't expensive and it's ugliness is so bad that I can't stand to look at it, I will restore. Examples are yellowed Apple keyboards/mice, super orange 1541 drives, etc.
Those rules have served me well. Granted, I'm biased as that I don't collect to make money. But I realize my large collection will have to be "dealt with" by my family one day so I might as well leave a little bit of profit in it for them.