Dictionaries document real uses of words. Because a dictionary is (usually) a finite size, the line on what is included and what is not has to be drawn somewhere. Generally, this line is decided on commonness of a particular usage.
I did the easy thing and searched Google for "tower of giraffes" to see how common that phrase was.
Most results were simply asserting that that was the collective term, but there was one actual use, in a newspaper headline: Tower of giraffes surprise [sic] woman Daily Mail, video
If Google's results are anything to go by, it's not really surprising that this use of tower hasn't made it into dictionaries. The same applies to jenny (apparently that's what a running herd of giraffe is called); romp (otters) and I'm sure many others.
There is a dictionary which seeks to be a complete historical record of English: the Oxford English Dictionary. It's unlikely that even they would include a couple of odd uses of a word, though: it would need to show some traction. It could be argued that if enough sources assert that tower is the word to use, that may be sufficient. This specific use of tower doesn't appear in the online OED, but its entry was last updated in 1913, with a single draft addition in 1993. Perhaps this use of tower has only become popular since then.