Hello Alan,
Provided that the true sample pitch is stored correctly in the sample files (or they are tuned perfectly to A-440/equal), and that each CODM ODF's Rank.Samples_RankBasePitch64ftHarmNumIfAssumedTunedToConcertPitch parameter is set accordingly to tell Hauptwerk where to read the pitch information, then having a different output sample rate set in the ODF shouldn't have any adverse effects on tuning, since Hauptwerk will re-pitch each sample/pipe in real-time according to the sample's sample rate and the output sample rate.
To see this in action, you can use 'Organ | Load organ ...' to load the StAnnesMoseley-ForLocked48kHzDrivers organ definition, which loads the standard (44.1 kHz) St. Anne's samples, but re-pitches them in real-time to 48 kHz for output. It will still play at the correct pitch.
However, it's very important that you don't set the output (i.e. CODM ODF) sample rate *lower* than the sample rate of any of the samples, otherwise you will potentially get severe aliasing because an anti-aliasing filter is not applied (for performance reasons). For example, if you set the ODF sample rate to 44.1 kHz and any 48 kHz samples were used and those samples contained any frequencies above 22,050 Hz (before or after any tremulant or other forms of pitch modulation) then those high frequencies would 'wrap around' to give unnatural (non harmonically-related) low-frequencies:
http://en.wikipedia.org/wiki/Anti-aliasing_filter
That won't be an issue if you set the output (ODF) sample rate at or above the highest sample rate of any of the samples.
However, even if some or all of the samples are 44.1 kHz and you set the output rate to 48 kHz there will be some noticeable loss of audio quality due to the fairly significant degree of real-time re-pitching needed.
Summary: you'll always get the best audio quality if the output sample rate and the sample rates of the individual samples match, although it's acceptable for the output rate to be higher than the rate of some of the samples. In neither case will the pitch be adversely affected, provided that the ODF and samples are formatted correctly.