Meant to be.
Fluff-wise, shield ally is like the shield-guardian's guard ability or similar effects. The eidolon is standing in the way, parrying attacks, and otherwise making it harder for baddies to hit its master. It cannot take these actions, like slapping away a swinging club or grabbing the summoner and yanking him out of the way of a greatsword swing, if it is unable to move.
Synthesist, however, is *inside* the eidolon, so even if the eidolon is paralyzed, it provides a shield bonus because of it's thick hide.
"But," you say, "It already has a natural armor class!" This is true, but it was a way to keep players from min-maxing their armor class in that particular way. The designers, it seems, didn't want eidolons using armor or shields and so the easiest way to discourage that is give a really low shield bonus, encouraging players to burn their money on other things.
