Yes unfortunately it's 100% possible for sceptacemia to develop during hibernation.
I would wake him slowly, hydrate & warm steadily. He needs an urgent vet visit for antibiotics (probably Fortum, it you can get it) keep tort warm 24/7 whilst he's taking the meds, as it will boost his immune system.
Your vet needs to check him over thoroughly as this illness is usually a secondary condition .
(One of mine had it due to a cracked plastron which let gram negative bacteria enter)
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