Normally, the engine itself uses proprietary signaling for its systems internally, but will present a standardized interface to the avionics.
Granted, plenty of de facto standards exist long before they're codified into a formal document. So maybe the Blackbird actually does use it, or something close enough for a dinky little converter box to do the job.
According to that Wikipedia page, out of the first 6 jets to officially use MIL-STD-1553, only one of them was a Lockheed product. That single Lockheed product was the P-3C, which was a retrofitted version of a plane Lockheed started making more than a decade earlier. To me, that suggests that, even if MIL-STD-1553 existed as a de facto standard at the time of the SR-71's contstruction, Lockheed probably wasn't using it yet.
All speculation, obviously. But the timeline leaves me with doubts.