Technically the only real need to have your intake manifold cleaned is for excessive build up around the EGR valve mixer and clogging of the port that goes from the cooler to the EGR valve inside the manifold.

If you are simply replacing the valve and servicing the manifold, scraping vacuuming of the large chunks of carbon followed by some scrubbing with an appropriate nylon brush and a chemical cleaner is all that is needed. As stated, the manifold is going to soot up again if the EGR valve is still in use therefore cleaning it to the point of being spotless is pointless.

Having the manifold hot-tanked is necessary when the EGR port is loaded with crust which is typically a combination of carbon and coolant that eventually breaks off and gets stuck in the EGR valve, hanging it open. This type of build up usually only happens with an EGR cooler failure that has allowed coolant to slowly leak into the cooler. Many technicians will have the manifold tanked when EGR coolers fail. In the past I have seen too many trucks get towed back in because even thought he coolers had been replaced and the technician (myself included) did a great job with the repair, the chunks will continue to break off and get caught in the valve unless they are completely removed.

I have never heard of any ill-effects of hot tanking. Blasting it with degreasers and chemicals and washing it out with a water hose usually brings poor results and unless you are hosing or pressure washing where the run off is drained into a waste collection tank of some sort you will be polluting and making a big mess where you are working. It can get downright ugly in fact. Don't ask How I know...

If you are in the EGR delete gang, having the manifold cleaned will only serve to make you feel good about it but if the EGR is removed from the equation the manifold will remain clean so in that sense it is worth doing.