Some feather dusters
I'm not arguing the logistics of the creature or how it showed up, was only looking for a solution to prevent overgrowth besides manual cleaning.
I think the reason you're not getting the direct answer you're hoping for is because no one has ever had pineapple sponges overgrow their system before
I wouldn't worry about them at all, I've never heard of them causing problems with pumps or anything else. Although I can't explain why you're seeing them just now in a 3 year old tank, they are very common in the dark areas of new tanks, and as mentioned will both self-regulate, and eventually disappear, in my experience.
For the time they are around, most consider them beneficial, although I'm not sure that's been shown conclusively, but that's a story for another thread
I don't know of any common aquarium animals that eat them, so the only reasonable solution is to try a sea turtle
And just to add, you can definitely have silicates in your RODI water, that's somewhat common. From what Randy Holmes-Farley has posted about this, silicates are one of the hardest ions for your DI media to remove, and one of the first ions released when the DI media is close to exhausted. Please see this post and the replies from RHF:
https://www.reef2reef.com/threads/silicon-silicates-in-rodi-water.840786/
I hope this helps and good luck!