Would a coolant flush fix it ?

Possibly, if the radiator is clogged inside. Does your engine temp get high too? But if you've never changed the coolant, you need to do it anyway. And makes sure the radiator fins are clean and not full of junk.

I know theses truck have 2 cooling system on for the engine and the other for the transmission

The transmission is cooled by the transmission fluid. Have you ever changed the fluid or filter? You didn't provide your mileage. See the FAQ for more info.

should I delete the system and straight pipe ?

Messing with emissions is illegal and could land you a fine.

Check your vehicle manual on millage schedule for fluid changes. Maybe the transmission thermostat is going out, as far as def systems I own a diesel pickup but I only have break down experience with commercial truck def systems. Commercial trucks will derate your engine when egr fault codes pop up.
Personally I would follow their experience and compare your last fluid and millage, because dirty trans fluid will cause overheating.
Diesels need a liitle more care than your average small four wheeler, spend a weekend studying your owner manuals regular maintenance chapter.
If you dont want a def system, find an old diesel pickup pre def age and rebuild the truck, who knows later you maybe able to sell it for a chunk of cash.