Oh hi. While I'm not an expert on aquarium grown plants I do happen to be an expert horticulturist working in the field of fresh water aquatic plants (for outdoor ponds mostly).
So I can tell you a bit about that the smelly roots thing.
In potted water plants "smelly roots" can be caused by several things.
1) Rotting organic matter.
You mistakenly put peat, mulch, manure, leaves or some sort of dead fiberous organic matter in your potting mix. It rots, it gets really nasty, it causes an anaerobic reaction and nasty nasty gasses, chemicals, algaes and bacteria grow in it. They cause nasty ammonia like stench.
With enough such material the entire body of water will be effected and the whole thing will turn black and bubble. And most everything in it will die (though oddly I've seen tadpoles not particularly care, so maybe axelotls don't either).
With only a little such material it will only effect the plant (in a bad way).
2) The plant itself is just a stinky plant
Some plants just have stinky roots. Same goes with regular terrestrial plants as much as aquatic ones.
It is also possible if your plant is slowly going backwards and dying (not unusual for an aquarium plant in cold water without enough light and all the other stresses) then it's own dead root matter could be causing a very minor anaerobic reaction in it's pot.
Most naturally stinky plants shouldn't be a problem, or if they are could just be subsituted with another plant. If your plants are slowly dying in their pots, well, you just need fresh plants or something more suited to the aquarium environment.
3) It's the fertilizer.
You probably won't have this problem in an aquarium because you probably shouldn't need or want to be using fertilizers in an aquarium.
But it is worth mentioning that a pot with some soil and fertilizer (any sort) in it if submerged can end up really rather stinky if you turf it back out again before the plant uses it all up.
Anyway as an outdoor pond person I can tell you now, potted plants is our preferred methodology we advise for growing fresh water plants in outdoor plastic and cement lined ponds. We just do it on a larger scale in bigger ponds with bigger pots, more fertilizer and different soil. Whatever stinkyness this adds is almost always outweighed by the significant benefits of the plant to water quality and pond life in general. Even in aquariums where you may ultimately only end up torturing and killing your aquatic plants they should be beneficial for at least a while (but you should probably remove them before they get too close to dead, a dead plant or even nearly dead plant in a small space is often a bad thing).
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