Any creature, organic or biomechanic, is comprised of multiple elements. We have AIR in our lungs, WATER in our bodies, FIRE in our mind, etc; etc;
Elemental powers are not limited to just the elements of the land, sea, or sky, they allow one to manipulate the internal elements of beings as well. Borderline psionics, if you'd like to call it that. Here's some examples:
Water — Control someone's blood,
Air — Control someone's breath, or take it away
Fire — Take away their emotions, or mess with their mind. ((The brain generates heat))
Earth — (Debatable) Enrich their body, or take their nutrients away
Stone — Control the bones, or force bone growth where it shouldn't. (Turning a person into a statue. A real thing btw)
Ice — Cool down their body, or force them into a fever.
Vakama having visions likely meant he was wildly powerful, incredibly strong—probably stronger than Tahu—yet that elemental energy could never manifest externally due to his fears. So instead, unknowingly, his powers were being used on himself.
If you think about it, Vakama's visions always triggered immediately in moments of stress. Where one's toa powers should activate. "But what about when he was saved by Lhikan's board? He wasn't a toa then!" Yes, but remember that Matoran have dormant toa powers, they manifest into their drives or sensations. Matoro was always a protector and willing to sacrifice himself to save others. Kapura was always trying to activate his mask power during MNOG. Vakama as strong as he is would have toa visions even as a Matoran.