Princess Celestia is almost definitely aware of Principal Celestia's existence at some point, but it is unclear if Principal Celestia is aware Princess Celestia exists.
In Equistria Girls, it is strongly implied that Princess Celestia is aware of the complications involved when visiting the alternate universe that Canterlot High inhabits. She forbids the rest of the Mane 6 from helping Twilight, which suggests that she's delegating this to only Twilight because she knows Twilight is not present at Canterlot High, which won't cause any undue confusion.
Of course, after Princess Twilight Sparkle recovers the crown and returns to Equstria, she has shared her experiences with other ponies. We know this because she explains why the rest of the Mane 6 can't help Twilight when she is about to return to Canterlot High in Rainbow Rocks, which they seem to accept and understand without objection.
So, if Princess Celestia wasn't definitively aware of Principal Celestia before then, she probably is now.
In Friendship Games, Principal Celestia seems to accept that the Twilight Sparkle that is competing in the games for Crystal Prep is not the same Twilight Sparkle that appeared to help during the last two movies, which had significant magical events occur at Canterlot High. It is lightly implied that she at least vaguely understands the difference. But if she's aware of Princess Celestia herself, it's not clear.