I think that thanking someone for sending the flowers is perfectly acceptable. You are not just thanking them for the flowers, but thanking them for the effort and cost involved in arranging for the flowers to be delivered to the recipient.
I occasionally thank my ex for sending me a letter or cutting. She has already told by phone or email me the news contained in the letter or cutting, but has taken the trouble to put them in an envelope, stamp the envelope and post the originals to me.