How common is the short "be" in American English
Solution 1:
I believe the distinction between the phonemes /i/ and /iː/ is a British phenomenon; it doesn't exist in General American. In General American, the vowel /i/ may vary somewhat in length depending on how much stress you put on it, whether it's followed by a voiced or voiceless consonant, and other considerations, but it's all the same phoneme, and there is no sharp difference between /i/ and /iː/ the way you find in some British dialects.
In some British dialects, Andy's and Andes form a minimal pair distinguished mainly by the length of the vowel /i/—see the comments on this entry of John Wells' phonetic blog. This is not true for General American, and I suspect there are no American dialects where this happens.
Solution 2:
The strong form of the verb "be" and the noun "bee" are indeed homophones in standard BrE and AmE. They are both pronounced as /biː/ (The Cambridge English Pronouncing Dictionary - Roach, Hartman, and Setter 2006; The Longman Pronunciation Dictionary - Wells 2008). The Oxford Dictionary for Current English (Upton, Kretzschmar, and Konopka 2003) gives /bi/ for AmE.
Try saying the be all and end all or What'll it be? It might help.
For those who like playing with language, try saying the following words and pay attention to your vowels (which one is the longest/shortest?):
bee - bead - beet
You'll be surprised. :)