It's a very personal choice. For my type of fishing, the last thing I need is something solid in the general area of my fast travelling rod tip.
It's also fairly seldom that the T-top actually affords you much protection from the sun. Most fishing is done early morning or late afternoon, sun angles that won't provide much shade.
I've heard a few people argue that a T-top provides a bit of lift whist underway, but, never having owned a boat with one, I can't say.
Whilst the T-top is on, try fishing with it, then take it off and try that.
Edit: Oh, lots of blokes use them to store rods (projecting upward from s/s tubes on the back edge of the T-top) but I keep my rods down under the gunnels and on the side of the console.