There really isn't any water
flow in this type of system so whatever sediment you'd get really shouldn't be an issue at all. The soil below the water line will get soaked and the soil above will wick it up. I wouldn't overthink it. I know it can sound too simple to actually work and we want to do all kinds of things to try to improve the design like with air stones and such, but the plants will start emptying the reservoir before too long so stagnant water really is not an issue.
While they're small I like to monitor the reservoir with a simple dip stick since I figure no need to add water to an existing pool that they're not using all of yet, but that only lasts a short time. Once I see good new growth I know they are drinking strongly and then I fill the reservoir every day and call it good.
Algae is going to be more of a function of light getting to the water so if you are using clear containers be sure to cover them with light blocking material. Paint, or burlap, or your cardboard, etc.
Coco is a good idea, but carries a different set of grow parameters.
@Bill284 can weigh in on this one but a good soak in clean water followed by a few good flushings should be enough I'd imagine. Coco does tend to lock up certain nutrients so those need to be supplemented more than in a soil grow and coco is never supposed to dry out from what I hear Bill saying.
The SIPs are really just a really efficient watering pot at the end of the day, so you would stick with whatever your normal nute routine is. Nothing much to learn really other than breaking the habit of watering through the soil. Our rule is only (or at least mostly) through the fill tube, by-passing the soil to fill the reservoir directly.