Any damage that would exceed barrier shield is not applied to your hit points.

So if you have a barrier for 300 and they do 280 damage, then there is no difference. You are left with 20 points of shield.

If they then 400, then you will lose all of your barrier as normal, but you won't take the additional 380 damage that exceeds the shield.

Voila. Now you have a reason to take it over heal. And as an assassin or burst mage you have a way to play around it but it requires a bit of coordination or atleast some timing: bust it with a smaller nuke that won't overkill the shield by much, and then throw your real nukes, or just wait for it to time out.

Even if you do throw a big nuke at someone who uses barrier, you will still consume the entire barrier.

The IDEAL best case scenario would be for barrier to prevent a bunch of small instances of damage and be dwindled down to 20-30 shield points, and then absorb a huge nuke to completely negate it. A carry that sees that his barrier is going to be depleted by the incoming targeted nuke might step in front of an ally to block a skillshot that won't consume the rest of the shield, just to maximize the effectiveness of the barrier for example. In other words, barrier has a higher skillcap.