I've learned recently, to my astonishment (I've been using Flask for the last 10 years and Bottle briefly before) that both names are puns on the WSGI acronym (which is pronounced "woos-ghee", and sounds similar to "whisky").

In Flask's case, it's indirect, as Armin admitted in the 2011 presentation (http://mitsuhiko.pocoo.org/flask-pycon-2011.pdf): "Wordplay on Bottle, probably a mistake".