Those are 'limber' holes and I will say I've been known to CAREFULLY take a Dremel to the extrusions they may be formed into to make them bigger, even on boats without floors. If cut large enough, I would think a long plumbing snake used periodicially from bow to stern should keep them unplugged. I would think a heavy pressure washing could make things worse.
But how about this for a WILD idea that I just thought of? To get the concept, in the 2" PVC electrical rigging tube on my big boat, I put in a 24' piece of heavy weed whacker line or monofilament, where the tube is only 10' long. I have a simple 2-1/2" round plastic block (1/2" thick, cut by a hole saw) tied to each end so I can't lose the line inside the tube. I use this
dummy line to help with the installation of new wires through that tube, by pulling wires from 1 end to the other. I coil the excess end up when not in use.
Do this in a similar manner, but use more than TWICE as long or longer than needed and put it in place through the limber holes, but tie in 'knots' every 8" to 12" that might help serve as little nubs to help clean the holes out. Flush with water just poured in from the bow.
Clearly the knots would need to be tied tight (use saliva or water before pulling tight) and be small enough to move through the holes. If you have room for them, a 'Figure 8' knot is good as it has length as well as width to them. And ... me thinks you might need 2 people to effectively do this, one pulling one way and the other pulling it back, to make it work. But hey ...
it could!
....
