The wording of Hagrid's comment about Time-Turners doesn't suggest that he actually knew Hermione had one:
“Even if yeh applied fer Time-Turners.”
Rather, he's likely just using a wizardly turn of phrase similar to the real-world phrase, "If I could turn back time". It's probably common knowledge that time-turners are ministry-controlled devices which can only be acquired by submitting a formal application, so a wizard who wishes they had more time might wistfully say "I should apply for a Time-Turner..."
In Hagrid's case, he's just emphasizing that he understands how busy they were: even if they had Time-Turners, they still would have had too much work to do to afford idly hanging around with Hagrid. Little did he know that by sheer coincidence they had in fact used a Time-Turner before.
Furthermore, if he knew they had Time-Turners and was shaming them for not using them to make a little spare time to spend with him, why did he mention "applying" for them? He would have said "Even though yeh had a Time-Turner," or something to that effect.