Most of the cookie bouquets that I have seen the cookies are not wrapped, but the basket is wrapped. Personally I think they would last longer if they were wrapped, but maybe they don't because it might take away from the bouquet, maybe its just a matter of preference.
They definitely do stay fresher longer if wrapped. I always wrap mine in cellophane, whether in a basket or a bouquet. It also helps to keep sneaky hands off of them (I have 2 young children/brats LOL) and I think it helps to keep the flavor in the cookie as well. 
I think it all depends on the intended customer.........if I'm giving a basket for ONE person to enjoy I don't wrap them individually.....but if I'm giving it to DH to take in to his job or someone for a party or something......I wrap each cookie then the whole basket.....that way they can pass out the cookies and some people opt to take them home vs. eating them right on the spot.
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