I thought going through navs wasn't a problem but was intentional and just no collision detection was added to them. Now that I think about it, they probably didn't add it to make it so you can't destroy them. You wouldn't want to destroy them in "As Lightning Falls", for example, because you might lose your way. In Derelect, you collected them in the first few missions. If you add detection, how could you collect them in Derelect? Will it add problems?
Yes ,navbuoys lack of collision detection is intentional and even more ,it's in tables ("no collide" flag).
It may be a problem if they lack this flag (setting them invurnable may be some sort of idea ,but you may sill collide with the buoy ,lack of collisions make easier dogfighting close to them) .
Though nobody stops you to release a mod that adds "GTNB Pharos#Destroyable" ,which would be essentialy the same Pharos ,but without the flag that removes collision detection.
And it's Derel
ict ,not Derel
ect.