The hitbox of the horse is larger than the hitbox of the boat, making it impossible to break the boat if a horse is riding passenger. You must kill the horse to break the boat.
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It is possible to get the horse out of the boat by placing blocks underneath and around the boat, removing the water from the enclosure, and then carefully destroying the boat with lava. Not really a practical workaround, but it will do if your favorite horse is stuck.

Confirmed for me.

Confirmed on OS X. (15w43c)
Also a "less aggressive" workaround from the lava solution... if a block of water can be placed 3-4 blocks directly above the boat-with-horse, the horse will dismount as the boat is forced under water. Both may then be interacted with as expected.

Still an issue in 15w44a. Can't right click the boat to enter it or left click it to break it,

Confirmed for 15w44b.

Still an issue for 15w45a.

Definitely confirmed for 15w45a. I did eventually get my donkey out of the boat, got in and then entered the boat before getting my donkey in. Needless to say, the donkey completely covered my vision. I laughed for about 5 minutes before hitting F5 and taking off.

For people who google for how to get their horse out and end up here, here's a short video of one of many ways how to get your horse out of the boat without killing it before the bug us fixed:
https://www.youtube.com/watch?v=aFqo3Kk7YvE
Cheers,
InnerBushman

Confirmed for 15w46a.

Confirmed for 15w47c. I also tried being under the boat but I still hit the horse.

Here is a screenshot of the hitboxes

Confirmed for 16w02a.

Getting it in 16w02a as well, though I've found if you put in a second passenger, such as a squid or a chicken, it offsets the horse enough to safely break the boat.

Confirmed for 16w03a

16w04a: It is now barely smaller; from what I can tell, you need to punch at the very bottom outside corner of the boat, which doesn't appear to be part of the boat (look with F3+B). Is still kinda annoying IMO.

16w04a: The solution IS NOT that horses can not be mounted on the boats ¬¬. Unfair to the players!.
This happens: So... I ride my horse, I find the sea, I let my horse, get on a boat, get to another continent but without a horse... Absurd.
The long explorations with transport in v1.9 ruined again.
I think this report should be reopened for "bad solution".
Sorry for telling the truth xD.

That's not the problem here, the problem here was that you couldn't interact witha boat if a horse entered it, so they made horses unable to enter to fix that.
If you can't cross a ocean with a horse and boat now, make a bridge, find other means of crossing the ocean.

16w04a / 16w05a: if you get put a horse in a boat (with commands), now you can interact with the boat ... The boat hitbox is below the horse hitbox (you hit the boat down and the horse will disembark)... So, it is not necessary that the horses can not be mounted on the boat 🙂. https://bugs.mojang.com/browse/MC-96536

Heh, like if I'd seen an iPhone... if a feature doesn't work just right, disable it all together. Fixing stuff cost money. Disabling is free! YAY!

The problem of not being able to transport a horse in a boat could be solved by making it so that the Frostwalker enchantment works when riding a horse, in that way you could ride atop a frosted ocean with your horse.

So if I understand correctly, the fix to this problem was to not allow entities with hitboxes larger than that of a boat enter it? So here I was transporting a baby horse in a boat, but now it grew up... What should I make of that? Apparently their hitboxes were tweaked a little allowing us to interact and consequently break boats from underneath. Still not to allow adult horse to enter boats while allowing baby horses in boats to grow into adult size makes no sense to me. And that while it seems like interacting with a boat (while troublesome from underneath) is possible?
So either this bug report or 96212 should be reopened.