It's Florida in the summer. Random stray pop up storms are part of life. You won't get rained on every day...probably. But there's a chance of storms most of the time. We typically go in June, usually for 14-17 day trips. We've had trips where we didn't get caught in the rain during midday once. We've had trips where it rained probably 8 or 9 of the 14 days during midday. It can vary from a 10 minute downpour where the sun comes right back out to a 4 hour rain event. On our most recent trip, we had maybe 3 afternoons out of 17 where there was some kind of rain midday, but it was usually brief. Another thing about it is that it could be pouring in MK but be bright sunshine in Epcot. We've had times where it was both pouring and bright sunshine at the same time...seriously.
It's not scientific I suppose, but we have found a good gauge of if it's going to storm in the afternoon is to look at the skies in the morning. If big white (non-storm looking) billowing clouds build fairly early, say by 10am, there seems to be a much better chance of storms midday. If the sky is clear or just has light wispy clouds, no rain.
I'd say be prepared for it, but no need to alter plans in advance.