He said they have material for three seasons. Doesn't mean the show will have three seasons. Material can be shortened, stretched, whichever.
Why is everyone always so hung up on Sir Patrick's age tho? The man is 79, not 100. He's still in great shape (he could probably wipe the floor with me), and while he has said that it's exhausting for him to shoot a television series, things aren't as they were with TNG where they were shooting 25 episodes in a row six days a week with 16 or more hour days - THAT one he could NOT do anymore, of course. But really, even if the schedule gets more demanding I'm sure everyone is more than willing to accomodate him (let him have his afternoon naps, etc) and make sure he's comfortable. It's for their own benefit - the more comfortable their lead actor is, the faster they get the scenes done.
MY prime focus when it comes to the whole "how many seasons" question would be "are they going to offer him enough incentives" - he recently said in an interview that he wants more challenges. THAT is what the prime question should be - whether the writers can deliver that one. This isn't TNG, again, where he had to go with what they gave him (and did the best he could with the material, I'm sure Rick Berman dreaded his 'yooo I don't think Jean-Luc would say or do this' phone calls after reciving a new script, haha) - he is an executive producer on this one, he's gonna have a big say in what happens and what does not happen.