Does destroying the Y-Wings at Walker Assault have any effect?

Solution 1:

Short answer: it decreases the y-wing run length, depending on when you shoot it down.

The first time I shot one down, I got curious about this and played around with it a lot. Here's generally what I've figured out:

Shooting down the y-wing will reduce that y-wing's amount of time it has contributed to the overall y-wing run. If you look closely at the graphic at the top of the screen during the y-wing run, you'll notice the "current" y-wing has a small cooldown that slowly runs out before the next one makes it's run.

That remaining time is what will be removed from the y-wing run if you shoot down the y-wing, meaning if you shoot it early in its flight, the whole time can be removed, but shooting later yields less of a reward.

Note: As mentioned by @Mufasa, there is also an achievement for shooting down one of the y-wings.