Yes, he boosts your skills. Perhaps it should be more explicit. In essence, he represents an exchange of the utility of extra items for the raw survivability of increased skill magnitude.
If you are using a shield but your fortitude skill is higher it does pick fortitude over shield when receiving a magic attack. A shield is certainly extra protection so in a tight spot, if just to stay alive until something comes off cooldown, a shield with fortitude boost on a fortitude character may come in handy.
I see that the text in game says the shield replaces the other skills, so I will need to clarify that. The idea is that if your character knows they are good at evading magical attacks they will evade, while if they are bad at dodging arrows they will try to use the shield to deflect them, etc.
There are other variables as well:
If your legs are heavily damaged, your defensive skills suffer due to lower mobility (actual value is fortitude*limb_effectiveness[legs]). A shield is wielded though, so its effectiveness is based on arm status instead. This also factors into which defensive skill you use, so if your legs are completely gone, wielding a shield would be the only chance to block/dodge attacks. On the other side, if your left arm is removed your shield skill becomes useless. Of course, extreme limb conditions are somewhat of a rarity.