No, it's not just a visual glitch as far as I can tell. However, the visuals seem to be glitching too. When I go down to the planet after having returned with a damaged Mako the Mako itself will be on fire but the Mako in the bottom left corner (where you, supposedly, can see the health of your mako) indicates that it's unharmed (i.e. it's all white). But if I save and load then the Mako in the bottom left corner will go all red as well and a full shield and an empty health bar appears. I didn't test what would happen if the Mako actually got injuried when it looked all white, though, so I'm not sure if it would act as if it had full hitpoints or no hit points.
Repairing it seems to fix the Mako. Due to an irrational dislike of using resources needlessly I didn't experiment all that much with that, though (so I didn't, say, wait for it to repair fully and then save and load to see if it stayed repaired).
Well, the key word there was my irrational dislike of using omni-gel. 🙂 I have more than 200 omni-gel so it shouldn't really be a problem. But... what if I need it later? I can get by if I simply avoid taking damage...
There was a popup that said -15 omni-gel when I repaired my vehicle. So apparently repairing your mako uses omni-gel. If the omni-gel that's used comes from a different pool then the popup message is misleading.
