I would not be too concerned if your fish and plants are both doing fine. My aquarium is not densely populated with rooted plants so I have similar concerns. What I did was use a small chop stick ones you get from a Chinese restaurants when dining and used a knife to make a point at one end(optional). Then I just poke into the dirt a dozen spots every few weeks to aerate the soil and release the bubbles. With a pointed chop stick I just rotate as I go down the substrate. Having a point helps to not push the substrate into the soil, at least that's my logic.