I think I've solved the problem. Despite what the shorewall-blacklist
manual seems to say, the traffic direction does not default to 'src':
it needs to be put in explicitly. When I changed the entry in 
/etc/shorewall/blacklist to

   # Whitelist port 9001 for TOR
   -                    tcp             9001            src,whitelist

the appropriate RETURN entry appeared in an iptables -L dump, and port 9001
isn't being blocked any longer, even from source IP addresses that appear
in the blocking ipset.

Shorewall version installed is 4.4.22.3-1, on a Debian wheezy box
(sorry, should have said that before).



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