@Artichuth
So first of all if you ever plan on reselling the guitar then know you won't get as much money out of the guitar as you spent on the modifications. However, if you like playing the guitar in general then it's worth it to play with modifications to make it even more suited to your style.
I never modified the cheap Radio Shack guitar I started with, but I keep it around as it was my first guitar. My MIM strat, though? I've played with all sorts of modifications over the years as it's my main guitar. I did pick up a pawn shop special to experiment with humbuckers before modifying my strat and found it doesn't suit my style, but otherwise? I've replaced sooo many parts on the strat over the years to make it my own.