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Simply put, yes. Condensing 2.1 channel signal into headphone-jack style connection is going to cut out a lot of the cool audio effects of your games.
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That's news to me. It's a only stereo signal to begin with, how could it lose "cool audio effects" if converted to a different jack? If you want discrete channels, you'll have to go for a digital solution (optical or coaxial).
EDIT: As far as I know, the Logitech speakers you linked to support stereo headphone jack input only, anyways.
Jam it back in, in the dark.