Should Sion be able to survive 3 seconds of attack without popping his shield? Probably not. Should his opponents be able to play around his shield detonation, even when he becomes a tank god in the late game? Definitely.
A tank's job in teamfights is to force the focus on the enemy team onto the tank so that he takes the damage that his team cannot afford to take. If Sion engages, the enemy team is likely going to focus Sion, but with a full tank build and the two second timer Sion will not take enough damage for the enemy team to pop the shield before they take 14% of their max health in magic damage. The enemy team will then not focus Sion because the magic damage is guaranteed, and try to hit the rest of Sion's team. With a 3 second timer, the enemy team has 1 extra second to break that shield, and Sion's opponents now have the opportunity to break the shield, forcing the enemy team to actually attack Sion so he doesn't get the damage. In this case the extra timer is good for Sion because it makes him a much more attractive target after he engages.
Sion is also at least somewhat guaranteed to get at least one detonation by timing Soul Furnace during his Unstoppable Onslaught so that he can detonate on landing his ultimate. You can do this now, and you can do this after the changes, but Sion players need to adjust so that they use Soul Furnace 1 second earlier.
Jungling with Sion will also hurt a bit, but just like his engagement pattern you can still clear with him. Sion players just need to adjust and activate W 1 second earlier (although the % health nerf is going to really sting for jungle Sion).
In most cases, Sion is going to really hurt with the extra second timer, but if players adjust themselves to adapt to Sion's new W timer he shouldn't feel it quite so hard.