When you do something that is linked to the trophy they will pop even though you passed them long before, example.

There is a trophy for killing 10,000 enemies.

When I started the PS3 vers. I had killed more than 10,000 enemies on my character from Vers.1, killed one mob and the trophy popped.
In other words, when you do an action that gives trophies, then it will check whether or not the trophy has popped. If it hasn't, then you'll get it.
Might take 15 sec or so.

In other words, yes you will get them, you just need to do an action/interactive with whatever gives trophies if you passed the requirement.