I think I understand your question to be: can you mute audio sources from the input files?
Answer: yes. You can either [a] not select that audio track for your job, so it will not be used at all; or [b] you can greatly reduce the gain on any audio track using the 'Input remix controls'. This will retain the track but make it functionally silent.
For HLS outputs, you have at least two options for including audio:
[a] audio content can be embedded in the video segments by adding the audio element to the Output which describes the video rendition. This is the default behavior for the first audio selector.
Or [b] you can have the audio tracks be separate HLS outputs (separate child manifests and segments). This is achieved by adding another Output to the HLS output group, and removing the video element from the audio-only output.
If you method [b], remember to set an 'Audio Group ID' for each discrete audio rendition, and remember to associate those Audio Group IDs with the Video rendition(s) by providing the names of the Audio Group IDs in the Video output configuration in 'Audio rendition sets' field. This field tells MediaConvert which audio renditions(s) should be included in the #EXT-X-STREAM-INF video lines of the manifest by including the ,AUDIO="Audio Group ID" parameter.