I used to delete them but found that the game just generates even uglier ones when it needs to fill roles. Townies that are made over seem to stick around longer (as in they don't get culled) if the game has already assigned them something to do in the world.
The one thing is though if you go down the makeover path, without mods, you'll never stop having to edit sims. Once in a while the game will generate a new librarian, as if all the ones you've edited weren't enough. And I found myself having to remake djs in particular so often until I got a mod to stop that mess. The game made those old djs I edited into unemployed townies for some reason. So there's that.
Oh, someone on this forum let me know of a feature that I've overlooked for years in CAS which is a button (the die inside a photo) that let's you swap out a townie's appearance for a random sim from the gallery, which is convenient if you need a quick sim that at least has all of their outfits together. Best thing about it is that the new sim maintains whatever role the game has given them. Be it a roommate, bartender, etc. So you've got a new sim with better aesthetics, and the same role.
Also, in terms of mods, I have a couple of bienchen's mods that effect the spawning of situational sims. For example I have three dj townies who I've made over. One of bee's mods stops the generation of other djs so I'll only see one of those three working at the nightclub ever.
I don't know if any of this helps, but I can say that my main save has gotten to the point were I can recognize certain townies, know what they do for a living and have not needed to initiate any major makeovers in a while. That is unless I have a sim move into a dorm, where the game spawns plenty-a messes.