We have the big brother of the Perkins 4's, twin 6.354's. And like previous posters stated, while fishing, they do load up a bit when you're idling for extended periods. But it would be seldom that we don't bring the engines up to full cruise speed, 2400 rpm for us, for an extended period of time returning to the marina and before shutting them down. This pretty well cleans them out.
Unlike an engine in a land vehicle, Perkins engines in boats are supposed to be propped to not exceed the manufactures maximum operating RPM at full throttle, 2800 rpm for us. Running them up to max. Intermittent operating speed for a reasonable period of time, does not damage the engines, (according to the Perkins manual I think it's 1 hour). You're burning more fuel, but not going much faster.
I don't know that running them 400 rpm faster for a few minutes really does much more to clean them out. I do run mine up occasionally for maybe 20 minutes, just to see if they heat up. That's often the first indication that you have a pump/impeller issue or cooling system blockage.
But you aren't hurting them either way. So if it makes you feel good, DO IT !
PS: There is a Perkins Operation Manual in the Library that covers your engines. If you don't have it, it's there to download.