By default yes — a 48 kHz audio track inside MKV becomes 48 kHz inside FLAC. If you need 44.1 kHz (CD-quality compatibility) the advanced sample-rate dropdown handles the resample with a high-quality filter (no aliasing artifacts).
Audio extraction is much faster than video re-encoding — typically 5-15% of source duration. A 1-hour MKV → FLAC finishes in 3-9 minutes on the standard pipeline; a 5-minute video finishes in under a minute.