I immediately think of three simple reasons for why run speed is good on a certain selection of weapons, the ones you're thinking of.
1. Dodging. Like SupaTim was saying, people in S/S+ really don't have perfect aim. If you surprise attack someone, sure, you can probably stand still and make sure your shots go straight. If you have to shoot at someone who will be trying to shoot you back, the difference between standing still while shooting and strafing is HUGE. It's extremely important to be able to do this, and Run Speed Up lets you do it even better, so when you think about it that way, it makes a lot of sense.
2. Pursuit. You may be able to easily close in on an enemy by swimming fast, but once you start shooting, you're moving much slower. By having Run Speed Up, you'll be able to maintain the required distance better. The Sploosh-o-Matic weapons are probably the very best weapons to demonstrate it. Without any Run Speed Up, I have a very hard time splatting enemies, because they're always just out of reach once I start shooting and manage to run or swim away. Then I slap on like two mains of Run Speed Up, and suddenly I'm too much in their face for them to escape.
3. More dodging. OK, not a very unique reason, but let me explain. The first point was about what you can do with more Run Speed Up, this is about what the game does when you have it. Percentage wise, on the paper, Run Speed Up and Swim Speed Up shouldn't make an enormous impact, and they probably wouldn't ... if the game was played locally. But alas, the game is played online, and there are a lot of issues with lag. A lot of the time, opponents won't actually be where the screen shows them. They'll usually be a little bit further ahead, so you'll have to make your shots hit the empty air in front of them, which of course is very unintuitive, not to mention difficult, because it can be very different from one enemy to the next. Anyway, the point is that, unlike with any other ability, the impact in the game made by Run Speed Up and Swim Speed Up will actually "scale up with lag".