If the client cannot access the files directly from a file share (using the same path as the Server), then Media Center must transcode and stream them to the client. This does result in slower load times from the client, and limits some functionality of MC on the client (Right Click > Locate > On Disk (External) does not work, for example). And the transcoding can result in playback quality problems, depending on the source file type and the configured transcoding settings.
JTV files are likely to transcode much more cleanly than TS files. Depending on what hardware is used to do the capture, live TV TS recordings often contain a wide range of encoding errors, stream breaks, and other minor issues. These can typically be corrected but often mess up transcoding processes.
It is best, whenever possible, to ensure the client copies of MC can access the files on a file share using the exact same path as is used to import the files on the Server. This can be accomplished in a number of ways, depending on your setup. If you'd like assistance configuring this, please explain where you have the files stored and how your Server accesses them.