I personally will try to lower my reputation from time to time to get a easier npcs then raise it again. If your reputation remains stagnant you get stuck fighting the same npcs.
When you get fresh npcs you can attack them as much as you like without all the buildings you didn’t attack turn to rubble. If you are trying to raise it go damage everything you want to demolish a tiny bit the first time then get it the second time. The buildings that you damage will always be there. If you are trying to lower it do the same thing the first time but make sure to get plenty of towers. Then send in a bunch of scouts several times (getting them all killed off) before finishing it off the last time with proper troops.
Now as for other players attacking you having a tightly packed colony is not always the best idea especially if your towers are obsolete. purposely leave several gaps of space in the middle of colony with a few walls blocking things off here and there. That way you can place land mines and have it so you can place them in different places so your enemies will not be able to completely avoid them. This is the best way to get rid of an enemy’s rovers and tanks if you have an enemy that constantly attacks you; that way they will be less successful in the immediate future. However if you are lowering it move your gold digger FAR off to the side double wall it move several towers around it and place land minds nearby. Let them destroy your well and capital and protect your gold digger.