By default yes — 48 kHz MKV audio becomes 48 kHz AC3 audio, 44.1 kHz becomes 44.1 kHz. If you need to downsample for compatibility (e.g. 96 kHz studio masters to 44.1 kHz CD-quality AC3) the sample-rate dropdown does this with high-quality resampling.
Audio demux + transcode runs much faster than video re-encoding — typically 5-15% of source duration. A 1-hour MKV -> AC3 finishes in 3-9 minutes on the standard pipeline. If the AC3 codec matches the source codec already in the MKV (common for AAC inside MKV / MP4), it is a pure remux and runs in seconds.