Do video re-encoding operations affect the container's audio file? Say I have a video file with contained audio file. So a container with audio and video codecs.

If I'm applying an operation in ffmpeg that will re-encode the video, such as applying filters or changing the container (assume it supports the audio codec) or video codec or whatever, does this also re-encode or affect the audio of the output file in any way?

Does the audio codec just automatically get a kinda pseudo -c copy command applied and translated over to new video file?

I'm trying to understand whether I need to specify a -c copy for the audio every-time I do an operation to the video part. Whether for the purpose of speeding up the operation or for avoiding quality-loss.

Like when setting an audio input and a video input and combining you need to specify a -c copy to get it to simply combine them. But I'm just a bit confused if you need to worry about it once the audio codec is already safely in the container and I'm applying operations to this video afterthefact.
In ffmpeg, copy mode for -codec / -c always needs to be expressly set.

So for

ffmpeg -i in -c copy out


ffmpeg will perform automatic stream selection and copy all those streams.

For

ffmpeg -i in -c:a copy out


ffmpeg will perform automatic stream selection and copy audio stream. Video stream will be transcoded.

I suggest you read the above link on stream selection fully. It covers stream handling.