Musepack StreamVersion 8 supports all sample frequencies.

First a table of some example sample frequencies usually used.
Explanation follows below the table.

Sample frequency	High Bitrate Profile	Low Bitrate Profile	Audiophile Bitrate Profile
2.8224 MHz SA-CD	resample to 44.1 kHz 32-PQF, use 32 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 63 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz	resample to 88.2 kHz 64-PQF, use 63 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz
192 kHz DVD-A	resample to 48 kHz 32-PQF, use 32 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 63 Subbands 375 Hz/Subband playback at 24 or 48 kHz	resample to 96 kHz 64-PQF, use 63 Subbands 750 Hz/Subband playback at 48 or 96 kHz
176.4 kHz	resample to 44.1 kHz 32-PQF, use 32 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 63 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz	resample to 88.2 kHz 64-PQF, use 63 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz
96 kHz DVD-A	resample to 48 kHz 32-PQF, use 32 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 63 Subbands 375 Hz/Subband playback at 24 or 48 kHz	64-PQF, use 63 Subbands 750 Hz/Subband playback at 48 or 96 kHz
88.2 kHz	resample to 44.1 kHz 32-PQF, use 32 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 63 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz	64-PQF, use 63 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz
64 kHz	resample to 48 kHz 32-PQF, use 32 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 63 Subbands 375 Hz/Subband playback at 24 or 48 kHz	resample to 96 kHz 64-PQF, use 44 Subbands 750 Hz/Subband playback at 48 or 96 kHz
48 kHz DVD-A, DAT, ADR	32-PQF, use 32 Subbands 750 Hz/Subband playback at 48 or 96 kHz	64-PQF, use 63 Subbands 375 Hz/Subband playback at 24 or 48 kHz
44.1 kHz CD	32-PQF, use 32 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	64-PQF, use 63 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz
37.8 kHz CD-ROM/XA	resample to 44.1 kHz 32-PQF, use 28 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 56 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz
32 kHz DAT-LP	resample to 48 kHz 32-PQF, use 22 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 44 Subbands 375 Hz/Subband playback at 24 or 48 kHz
24 kHz	resample to 48 kHz 32-PQF, use 17 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 33 Subbands 375 Hz/Subband playback at 24 or 48 kHz
22.05 kHz	resample to 44.1 kHz 32-PQF, use 17 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 33 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz
18.9 kHz CD-ROM/XA	resample to 44.1 kHz 32-PQF, use 15 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 28 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz
16 kHz	resample to 48 kHz 32-PQF, use 12 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 22 Subbands 375 Hz/Subband playback at 24 or 48 kHz
12 kHz	resample to 48 kHz 32-PQF, use 9 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 17 Subbands 375 Hz/Subband playback at 24 or 48 kHz
11.025 kHz	resample to 44.1 kHz 32-PQF, use 9 Subbands 689 Hz/Subband playback at 44.1 or 88.2 kHz	resample to 44.1 kHz 64-PQF, use 17 Subbands 345 Hz/Subband playback at 22.05 or 44.1 kHz
9.6 kHz	resample to 48 kHz 32-PQF, use 7 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 14 Subbands 375 Hz/Subband playback at 24 or 48 kHz
8 kHz	resample to 48 kHz 32-PQF, use 6 Subbands 750 Hz/Subband playback at 48 or 96 kHz	resample to 48 kHz 64-PQF, use 12 Subbands 375 Hz/Subband playback at 24 or 48 kHz

You must distinguish between native and non-native sample frequencies.

Native sample frequencies are encoded without resampling, non-native with high quality resampling or using special designed PQF subband splitter. Resampling is done using rational ratios a:b with very small a and b.

Although the file format supports native frequencies up to 65.535 kHz for 32-PQF subband splitting and up to 131.07 kHz for 64-PQF subband splitting, the actual implementation only supports 44.1...48 kHz for 32- and 64-PQF and 88.2...96 kHz for 64-PQF. This makes tuning easier, and >99% of the HQ audio material is sampled with these frequencies. Maybe later the native 32 kHz sample frequency is supported when urgently needed . . .

Files encoded with 64-PQF can be played with half the native sample frequency, files encoded with 32-PQF can be played with double the native sample frequency if wanted.

Encoding with 32-PQF and 44.1...48 kHz is called High Bitrate Profile and is usually used above 100 kbps/stereo pair.

Encoding with 64-PQF and 44.1...48 kHz is called Low Bitrate Profile and is usually used below 100 kbps/stereo pair.

Encoding with 64-PQF and 88.2...96kHz is called Audiophile Bitrate Profile and may contain frequencies above 22.05/24 kHz if necessary/requested.

Low Bitrate Profile has increased spectral resolution, reduced temporal resolution and reduced coding overhead. It can be compared with downsampling used by MP3 encoder, but the file format is still able to encode high frequencies if urgently needed. It is used for low quality profiles where transparent encoding is not possible and the main task is to make a good trade-off between the usual codings artefacts to get a good quality. A increased spectral resolution, reduced temporal resolution and reduced coding overhead you can also find with the 32-PQF and a sample frequency of 32 kHz and below. I don't know anything about the drawbacks of this . . .