Users wanting to connect to JTAG can make an adapter to connect to JTAG device. JTAG uses 10-pin header, but there are not 10 signals, only 4 or 5 and then power Gnd.
Headers - I'll check that - have to redo the schematic to split them off.
ISP header is at the standard location so the one shield that plugs onto it can use it.