Firstly, it IS possible to have the crank bolts too tight, but on a square taper crank, I've been told that "too tight" is when the crank splits at the hole for the spindle. I've never tried to find out, that may be complete rubbish.

Now the knocking. How often do you get the sound? Once per revolution of the cranks? Of the wheel? If neither of those, is it regular, and does it vary with your speed?

Check your cranks and rear wheel bearings for play. The rear wheel may have slight play in it because some SA hubs are designed to (the classic AW did, not sure about the S3X, that's more closely related to the 5-speed than the regular 3-speed)

Also, check the adjustment of the gear cable. I'd assume that a fixed-wheel hub would make noises under coasting as well if it was misadjusted, but it's under a lot less load when it's just driving the freewheel round, so it could be that.