Shotos and Terry can have some real trouble against projectiles users, but they have some weapons to deal with it.
You have to be confident with your tools and use the maximum of your character's agility. Firstly, and this apply to most characters, don't forget a projectile can be avoided with several methods : Jumping, shielding, dodging, rolling, parrying (probably the hardest tho), crouching (sometime), hitting, catching (with objects), air-dodging ; these are the tools you got with almost everyone in the cast. Virtually everybody can do it, but some options are less effective with some characters : Jumping with a character that have a low full jump asks for more timing and can be way harder ; on the other hand some characters have options more effective than most of the cast. Snake can pass under many things while crawling.
Before everything, you have to think about all of this when fighting a projectile character. Against mid level or beginners, this will be enough.
Good players will know all of these possibilities, and you'll have to surprise them, varying your methods and follow-ups. Patience will become the most important thing there. As someone said before here, at some point the opponent will lose patience too.
Terry happens to have several way of moving around, with his specials doing some weird movement. This can be used at your advantage in some situational conditions. Maybe using the power dunk and crackshoot can be a way, and forcing the opponent to react with some power waves alongside your movements can also put him in a urge.
Still, with all of this, it's an hard match-up. I'm playing Ness and even with all my projectiles, I don't like facing a Link (I feel more confident against Samus but I might never have played with a very good one). Don't forget these are not so fast characters (except Link when it comes to fast fall), you might need to capitalize on the rare moments you have advantage.