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It seems that at the present time the updater service found in su.apk fetches new su binaries over http and checks that the md5sum of the downloaded binary matches that defined in the json descriptor. [0]
I would like to suggest that future upgrades hashsums are distributed through su.apk via updating su.apk in the android market (and or the binary as well) which can be used to verify a su binary is legit.