Usually I do, but a lot of the times, I waste time trying to think of a name that truly fits the Pokemon.
I wasted the good part of an hour trying to think of a nickname for my male Shellos. I couldn't nickname it Mari, Shelly or Aqua, those are girl nicknames. I couldn't name it Shelldon, it sounded weird.
Eventually, I thought of the name Aquos, which is the name of some TV company that [supposedly] produces crystal-clear visuals. Plus, it sounded like Aqua, so I stuck to it.
And personally, I feel like Aquos would've been a better name for it than Aqua.
So, even though it is a bit of a time-waster, I've nicknamed my Pokemon. It makes them unique.