I see the microwave tank aura around the EMP patriots, what do they do?
The tooltips don't give any insight.

Thats there to cook anyone nearby with damage over time hence hijacking a tank near it or attacking it with terrorists is not really viable.

Since it's a microwave beam, why no effect? (Whoops, there is no ping effect)

On a side note, is there much of a different between the damages of the Pop-up Patriot and the EMP Patriot?

Pop-Up is a stealth defense, EMP excels vs vehicles. Also, I think the Pop-Up does better damage vs infantry with its missiles but i'm not completely sure about that.

Because if it had visuals, then it wouldn't work as a trap Also it would lag the game if you has a lot of patriots.

EDIT: Though I do agree, that there should be something about it in the tooltip.

Why not just use it and find out

In older versions, it was a blue pulse around the patriot. May bring that back, and I will definitely be adding something about it in the tooltip.