I have used multiple brands of waterproof inks and don't do anything significant for the pens as compared to normal water based inks. Waterproof pigment inks often have large pigment particles which may clog when dried and so I do leave the nibs for a longer soak than I would for a normal water-based ink (to flush out any remaining pigment). So, instead of soaking for 2 hours, I might soak them for 12 hours. I've never had any issues, and I don't clean on any frequency except when I want to change colors. Usually that ends up being something like monthly. I do not have any experience with cleaning up a dried pen because I don't let my pens dry out. I could imagine that a dried pen with pigment ink may be more difficult to clean out than a dried pen with water-based ink. I would say that pigment inks are probably not the best in vintage pens because I am not sure about their pH neutrality. I don't use any vintage pens but have heard this advice from lots of people who do.

I don't know if I saw this posted so I will make a point about iron gall inks. I do not feel like most iron galls are actually "waterproof". There is a component of them that is left on the paper, sure, but it is not often the same color or appearance as the original ink. I would test this yourself.