1. Deprecated directives. If a configuration includes the deprecated "rewrite_subject" directive, will spamd barf? Or ignore it? Or something else? What about spamassassin?
Based on past experience they generally don't cause problems on their own, but if the parser gets confused, they can help make it more confused and cause more lines of config to be dropped.
I'd use spamassassin --lint to find the deprecated options and fix them.
2. Spamd/spamc protocol. Will a 2.6 spamc communicate properly with a 3.0 spamd? What about a 3.0 spamc with a 2.6 spamd? If they're not compatible, what are the failure modes?
I'd not recommend mixing versions, but based on the code the protocol version for spamd/spamc hasn't changed.
Mail-SpamAssassin-2.64/spamd/libspamc.c:static const char *PROTOCOL_VERSION="SPAMC/1.3";
Mail-SpamAssassin-3.0.0/spamc/libspamc.c:static const char *PROTOCOL_VERSION = "SPAMC/1.3";
3. Deprecated command-line options. Will the options deprecated after 2.6 be ignored, or will they cause failures? What about options previously deprecated, like '-S'?
I suspect they'll be ignored with a complaint to stderr, but this is a suspicion only.
