Ok, if I go with an "EGR Cooler" delete kit, what effect does the hot exhaust have on the still controlling EGR valve? With the "block off plates" the EGR valve still operates but no exhaust gas is being introduced to the intake.
Lets look at the options available.
Below you will see a pic of the up-pipe that comes with a delete kit versus the stock up-pipe. The stock up-pipe is the lower of the two in the pic. Note the flange that your existing EGR cooler connects to to allow the exhaust gases to flow through the stock egr cooler, and the absence of such a flange on the delete up-pipe. Since a delete kit does not attach to the exhaust, there will not be any exhaust gases being fed into the intake and the egr valve. The valve can be left in place in the intake, since there will not be any exhaust flow for it to regulate. The EGR valve should be left in the intake (IMHO) because there is some evidence that unplugging the valve can result in issues with your cooling fan.
The pic above is only if you go with the delete kits, and NOT the one from bulletproof diesel. The egr cooler delete through bulletproof diesel would still utilize the stock, existing up-pipe. The bulletprooof diesel egr cooler delete appears to be an egr cooler but is solid and does not have passages in it to allow the exhaust gases to flow through it. It is recommended that, should you have an 05-up engine, you should still remove the existing up-pipe and use a tool like a dremel to remove the "egr cooler scoop" that is internal to the up-pipe and was put there to direct as much of the exhaust gases as possible through your egr cooler.
A pic of a popular delete kit:
The "U" shaped pipe is installed to redirect the coolant flow from the top of the oil cooler back into the bottom of the intake manifold.
A pic of the bulletproof diesel egr cooler delete: (This type is called a "sneaky delete" since it will appear stock for a visual inspection)
Look internally to the cooler in the pic. It is solid inside and that is what will block the exhaust flow. Unlike the kits that totally remove the egr cooler from the engine.
Coolant enters this type of delete the same as the stock unit (through the long pipe attached), but since it is solid inside and blocks the exhaust flow, it can not leak into the intake.
Explain how a weld failing will get coolant into the intake, I am kinda lost on that one. It looks to me that if a weld failed then the worst thing would be an external coolant leak.
The reason behind everyone deleting the EGR cooler is to stop the egr cooler failure from resulting in head gasket failure.
There are two ways in which this could occur. The first is that the failed egr cooler will leak coolant. When the PCM commands the egr valve to open, this coolant is sucked into the intake manifold and the coolant is then sucked into the combustion cylinders. The coolant will boil and create steam and steam pressure. This pressure will create much higher cylinder pressure than the stock TTY (torque to yield) head studs can handle and they stretch. That causes the head gaskets to blow.
The second way a failed EGR cooler can harm your engine is when the coolant flows the opposite direction. When you shut the truck off, the pressure in the cooling system can be sufficient enough to force the coolant out of the failed EGR cooler. The coolant will flow down the up-pipe that the EGR cooler connects to, and enter the exhaust manifold on the passenger side. If the exhaust valves just happen to be open, coolant can fill the cylinder. This will cause hydrolocking of the engine.
If you were to weld plugs/plates/whatever over the exhaust openings of the existing egr cooler, and your weld fails, it would act much like a failed egr cooler and could result in what was just outlined above. If you choose this method, make sure that whoever welds the egr cooler knows what they are doing. Also, it is STILL recommended that you remove the up-ipe on the passenger side and use the dremel to remove the egr scoop, then reinstall the up-pipe.
PREPOSTING EDIT: You might get it now, but heck, I already typed this all out, so I am posting it anyway.