Retired_Hippy explained it very well in post #1, so it seems to me that posters 3, 4, & 5 are just looking for reassurance. :o)
First of all, ferry schedules DO NOT change a lot, except to account for higher demand during peak season. Occasionally bad weather forces cancellation, just as with any other transport system (e.g. the many flights cancelled this winter due to snowstorms in eastern U.S.). Weather cancellations are very rare, though, only a few days over the course of a summer.
The two primary ways to get from Mykonos to Santorini are:
1. SeaJet 2 to Paros departing 10am, connecting with Blue Star to Santorini 11:55am, arriving Santorini 3pm.
2. FlyingCat 4 direct to Santorini, departing 2:55pm, arriving Santorini 5:35pm.
Although route #1 involves takes longer and involves a connection in Paros, it has a few advantages. First, if it is cancelled or delayed, you have another chance to get to Santorini later in the day on route #2. Second, all but the first 40 minutes is on the much larger Blue Star, smoother in rough weather, and allows you to stand on the outside deck for views and photos. Third, you arrive on Santorini earlier in the day.
The advantage of FlyingCat 4 is the shorter direct journey.
For FlyingCat 4 we use http://www.ferries.gr/hfd/ as a reference, because it is published earlier, and clearly shows times and prices. Like Retired_Hippy, though, I never book my ferries over the internet (actually I did once, last year, just to see how it works). It's easy to buy your tickets when you get to Greece, and there are normally plenty of empty seats except from mid-July to late August, and around Greek public holidays. If it makes you feel more secure, go ahead and book.