I'd be very, very concerned. The clitoris is NOT supposed to contain the urethra. (Sometimes a surgeon will make the hood out of leftover urethral tissue, but that's different; it's stuff that was going to be thrown away otherwise, not the actual functioning urethra.) A normal clitoris does not have a hole in it, either. Heck, it's not even supposed to be particularly close to the urethra; there should be an inch or two between them, with the clit at the very top of the vulva and the urethra situated *just* above the vaginal opening.
It almost sounds like what's done to modify the new penis in a trans male surgery, which is... not what you wanted!
Basically, that's probably not dangerous but it is anatomically inaccurate, undesirable, and really weird. I hope it does turn out to be just an odd-looking intermediate healing stage, and not an actual hole there. Good luck getting it taken care of.