Update: BIP91 has activated without issue. BitMEX is again crediting deposits after 1 confirmation.
Starting 24 blocks before BIP91 activation (in 3 hours, or about 02:30 UTC), deposits will require 6 confirmations before being credited to your BitMEX account.
This change is for the safety of the exchange and will be reverted as soon as there is no longer danger of a blockchain reorganization.