Plants that grow as both aquatic plants and as terrestrial plants are essentially swamp plants, that need to be in wet soil when not submersed. I don't think you need to worry about molds and fungus, as long as you don't keep the humidity at 100% all the time. Keep a small area of the top open all the time, maybe a square inch. The problems I have seen here on the forum were from keeping the water too high, so there are very shallow ponds scattered over the substrate. Those are stagnant water, very subject to problems. The substrate should be wet, not underwater.