I don't think this will be a problem. Some of the larger game services have been using the fs_game switch with MoHAA and it has been working. If everything works as it should, your mods would just go into a directory under your main directory and you would run them by setting fs_game in your command line. If you want more info, do a net search on Q3 mods and look at their installation instructions.
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"If your philosophy does not produce corn, I don't want to hear about it." - Red Bear