Granted but how do they benefit from it? Destroying Megaman just puts the rest of the robots on alert since hey, a huge friggin beam just shot down from the sky and atomized their hero. They have space platforms and ships and such, they would mount an offensive against the Yeerks and its right back to it being a simple fight just minus Megaman, still there's Zero, every boss and the masses of minions to throw themselves at the Yeerks in wave after costly wave so being subtle isn't exactly a bad thing here.
The Yeerks gunning Megaman with the pool ship gets the job done but why not just learn to control him instead? That costs less and gives them shock troops superior even to Hork-Bajir because no Yeerks need to die in the heads of a Megaman robot, and as we all know the little ones regenerate when they're out of sight, walk off screen and when you come back there they are, the punks.
So while the Yeerks can easily just blast the whole planet from pace and probably get tangled in a minor space battle, maybe lose a pool ship if megaman's robo-buddies get insanely lucky but far more likely lose just a few squads of bug fighters, and they do this why? They have to have a motivation, otherwise unless they thought the robo-thingies were a threat to them they'd just keep flying through space and leave the little planet alone.