It isn't designed to show you the best missile design and have you use the one at the arrow, it's designed to give you a list of options. The arrows are just to show you where the maximum hit percent chance is, but the actual design you use is up to you. If you want a faster missile just go up the list to a desired speed. It gives you the hit percentage at that speed and all the numbers for it. The little mark just shows you the maximum possible amount of maneuver you'll want to put in, since after that point your missiles get worse instead of better.
You just input the desired warhead, desired range, desired size. Then it shows a list of the possibilities with those numbers and using the rest of the missile space on speed and maneuverability. At the top of the list you devote all the space to speed giving you the fastest speed but poor accuracy, and down the list you begin sacrificing speed for accuracy by adding in a little bit to maneuverability. You just look through the list and pick the one you want.
At high maneuverability tech levels (especially if your engine tech is falling behind) you can get missiles that, while having a higher hit chance, are slower than your target and thus would never have a chance to hit them unless they were flying toward you - this just means you have to use your judgment on which design to actually pick. I haven't tested to be sure, but I believe missiles like that actually would work if the target was coming straight at you (and have a higher hit chance, since it maneuvers better to get in the way of the target coming at you), so they are viable missiles - just not optimal if you need them to be able to hit targets that are moving away at higher speeds. In those cases you would need to sacrifice hit chance to get faster missiles.
If the target is going to be running from you at high speeds your effective range would also be seriously diminished since your missile is effectively traveling at the speed difference (say target is 99000, missile is 100000, relative to the target the missile is only going 1000) and yet using fuel for the full speed. So if your target is 99000 and your missile is 100000 your missile's effective range is actually 1/100th of the listed value, since it will have to travel 100x the distance to close on the target while the target flees. It will also have ample opportunity to shoot down the missiles. I've never found myself in a position to be fighting an enemy with ships that moved nearly as fast or faster than my missiles, though.
