No covering up is necessary - they didn't even get fully changed for bed. Ted's used to sleeping at least partially dressed anyway, and the past few days he hasn't gotten dressed in more than he could comfortably sleep in, beyond pulling on a sweater or hoodie. (He does kind of look forward to having a reason to get properly dressed.)

"Hey," he greets quietly when Sherlock enters, and closes his laptop and sets it aside. "You sleep alright?"