How does a Touchstone (s2p) file indicate whether it should pass or block DC?
The short answer is it doesn't. You can find the Touchstone 2.0 file specification here: http://www.ibis.org/touchstone_ver2.0/touchstone_ver2_0.pdf. There's no provision for specifying DC behaviour.
Indeed, at least one simulator I've used that supports using S-parameter files in a transient simulation where DC behaviour is important has a check box to specify whether to consider the component an open or short at DC.
I agree that if the software doesn't support that, a large ideal parallel inductor or large ideal series cap should do the trick.