Does destroying the Y-Wings at Walker Assault have any effect? Like does it decrease the time the rebels can attack the walker? And does it matter if you do it after or before the Y-Wings fire at the walker? Before is really hard to do though.
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.