Great point! My Merc Racing 600SCi's in the 388 are closed cooled, and have alum. heads, but my 572 in the Talon is raw water cooled and have the Merc Racing rect. IRON heads. I flush both engine types, for 10-15 minutes each, BUT I would be leary of running alum. heads on a engine with raw water cooling in salt/brackish water.....

I do have aluminum heads and intake. I do flush extensively afterwards, but running in salt water should be avoided with these items?

Closed cooling is always better then open for reasons others have pointed out along with you can run them at 180 degrees. The only bad is don't do it with an engine which has time on it without a rebuild. The stuff which breaks loose every so often currently goes right out the exhaust. With closed cooling it will start clogging things up. There is a Merc service bulletin on the subject and recommends no more then 50 hours.

Would it be feasible to put a filter somewhere in the closed system and collect the debris on an older motor conversion?

You can get alum heads with a "Hard Coating" on them for salt water running, but I don't have any experince with that set-up, so I can't speak as to how they do in salt water.... I just like the idea, and have try to avoid it on all (14) of my boats..... But I have a Dart Hi-rise Alum intake, on the Talon engine, and I just flush the heck out of my engines, 10-15 minutes......

Not the expert, but was at Eddie Young's shop two days ago and he had a set of aluminum heads which looked great except the water ports had some bad erosion on them. IMO you can do a lot of flushing but to get it really flushed good, the thermostat needs to stay open, which we know it's not designed to do that. Eddie grew up in Louisiana so give him a call or PM him and see what he tells ya

Again not an expert but I spend most my time at iboats. Only reason to bring it up is iboats is I've seen a lot of folks which have done it with bad results later. Only ones which worked out were on very low hour engines for salt, and a bit higher in fresh. Only seen a few mentioning filters but have not seen anyone coming back to close the threads with good or bad news. Don't know if a filter would help or hurt.