All three of the forms you gave are fine and none would cause any confusion.
It may be that the third form, "I hope your holidays are great", is slightly grammatically incorrect, since you are hoping for something in the future but using "are", the plural present tense of the verb "to be". However, it is a very common construct, at least in spoken English.
In fact, consider the following two alternate versions of the forms you gave:
Enjoy your holidays! I hope they'll be great.
Enjoy your holidays! I hope they're great.
In this case, the first form, while possibly more "correct", feels awkward, while the second form flows nicely and is, for me at least, the preferred format.