Previously I probably should have explained the rationale for not vacuuming the substrate in a planted tank. I did allude to the organics, and this is in fact the reason. It isn't as critical in a high-tech set-up where you add diffused CO2 and daily nutrients, but for those of us with natural or low-tech systems the substrate should be left alone. The waste that collects in the substrate is of course organic in nature, and as this is broken down by snails and then bacteria, dissolved organic carbon is released. This is the prime source for CO2 in a (natural or low-tech) planted tank. The CO2 released via respiration of fish, plants and bacteria is much less by comparison. So by doing any sort of cleaning of the detritus, you are removing a major plant nutrient (carbon).
Aside from this, there are other nutrients being produced from the organics. It is possible to never add nutrients via fertilizer, since everything the plants need is available from fish foods and water changes. Most of us have more plants than this will support, or we may have very soft water with no minerals, or the fish load may be minimal which obviously means less fish foods ending up as organics. But nevertheless, the value to the plants from the waste breaking down in the substrate is significant.
Another aspect is the host of bacteria. There are more bacteria, including the nitrifying strains, in the substrate than in the filter. A healthy substrate is important for healthy fish. There is much more in the way of bacterial processes involved than just the nitrifiers we all think/worry about. Maintaining a rich substrate provides the complete biological system that means healthier fish.
Now, having said all that in defense of leaving the substrate alone, there are some situations when this has to be handled differently. An excessive organic build-up causes primarily cyanobacteria, but various algae can take advantage too. An aquarium with too many fish for what the system can easily support will soon have problems, and removing the organics is key here. But when we are dealing with balanced biological systems, it is best to leave nature alone to do what it can do better than we can.
Byron.