The 200 ohm resistors are used to provide short circuit protection (and they slow down the edges). The 10k resistors are chosen to provide adequate pull-up (which almost any value will do), not present much of a load to the programmer and not provide much of a voltage divider to the JTAG signals. 10k is just a common value.
If I couldn't figure out whether to use 3.3V or 5V for the JTAG programmer, I would put a voltage selector jumper near the JTAG connector. Problem deferred...