I would have to guess that same goes for civil aviation I can say for certain from experience that birds cause a lot of damage to military aircraft every year.At most airbase they have various systems in place to try and scare birds away like trained hawks or they will go out and fire blanks to scare flocks away.
I saw a C-17 collide with a huge flock of of swifts or swallows

in Germany once must have killed 75 or more and they came right back to check for damage the front end of the plane was covered in bird bits none got ingested by the engines though.Now if that flock had hit a little left or right it might have taken out one or two engines on one side which would be a challenge for any pilot not to crash seeing as the impact was just as the C-17 lifted off.