If you have additional health from runes/masteries, it is technically a buff. I was a bit miffed at first too, but then a friend and I went over the numbers. It's an almost unnoticeable buff to his early game (I think with my current set-up I only gained 1.26 points on the shield at level 1), but a big one to his late-game.
The only problem is that -as you said- his early game is when he is weakest. He needs more of a buff for that period, rather than late-game. This is a nerf to the shield's base, but a pretty big buff to its ratios/scaling. It used to go off of bonus health. Now it goes off of max health, and it scales higher as you put points into it.
I will agree, this is an odd direction for Nautilus buffs, but I do like that Riot actually recognises that he needs help. More could definitely be done though, like working with his insane mana issues.