Haha, I don't think realisms can play much a role here. Technically one person on a horse, charging in a group of 50-80 people, slashing a couple heads, safely run out, and repeating the process until they enemy army is heck confused and about 1/4 dead is very unlikely in the real world; we can probably drop the realism about how accurate people can actually throw their weapons (although, to be honest, professionals actually DO tend to throw very far and accurately)
Plus they are not homing; it's just that when you do see javelins flying, it often means you are fighting a Nord group or sea raiders. Their infantry are virtually all equipped with javelins. So we are talking about usually 10-30 javelins flying at your direction as you run "towards" them. Not surprising to see yourself at least get jabbed 2 to 3 times, according to statistics.
To be fair, each person only has about 4 throws, so it is not that overpowered imho. If you are really frustrated about how much damage they do, reduce the difficult in game? If you insist on playing realistically with relatively higher difficulty, grab a shield, and try to run in curves such that you have better chance of dodging javelins instead of going towards them like you are invincible (because in real life, you are not invincible; one jab in the head and you go byebye. Since there are about 15 flying towards you, it's not unlikely that that happens, unless you can block flying spears with your sword. :p )
And yes, I do think the speed on your horse affects the opponent javelin damage. If it works for sword and axe, I don't see why it wouldn't work for arrows and javelins (in this case, I was the one cutting, usually the horse. Lol). So, running towards javelins make you that much easier to be killed by them. Have you tried to go around them and hit their behind instead?