Hmmmm. Why not just try both? I really doubt there will be a difference for CDs.
Actually no, HDMI is not just for multichannel sound. Modern HDMI can have up to four I2S streams, one spdif, and more than one 8bit video channel. It's the only standard interface that CAN carry I2S as I2S in itself has no standard connector.
OK, that said, if it's a modded player with a great built in DAC, just use the analog for two channel music enjoyment if it sounds better to you, otherwise don't worry about digital audio coming over HDMI versus a Coax and SPDIF that probably is not the proper 75 ohms anyway.