Yes and no, Tim. If the player has the decoder, it's not an issue in the sense that you do have the required functionality then in your setup to enjoy.
But it also depends on the implementation how good it works in practice. If too much of the decoding of a new multi-channel codec (i.e. DTS Master) has to be done by the player software (in addition to image processing: decoding, de-interlacing, rescaling, etc.) a timing problem might develop in some cases. Note that some of the streams have to be decoded even if the user isn't selecting them (wiring them through).
The full and definitive DTS Master codec was finalized relatively late (July 2006) and proper hardwired decoding chips may be rare at the moment.
So, when fast decoding hardware gets available: that can relieve the player's processor, but that's also the very moment of course that we will start to see decoder/receivers with the support for the codec in question.
Perhaps the PS3 is an example of a player having a hard time when having to perform all those time critical tasks, because it's based almost exclusively on processor power, less on dedicated hardware for this specific purpose.
(I personally think that the decision of using uncompressed audio on some of the latest BD releases instead of a lossless compression has more to do with this "problem" than anything else. And currently there's enough space on a BD50 in the wasteland of unused bytes to make this solution a cheap one.)