According to Robert Reed in his book "Colt .45s, a Six Gun Salute" the team was originally to be known as the "Colts" but Robert Kirksey persuaded the Colt Firearms Company to allow the HSA to append the ".45s" to the name in 1961 before the team started play in '62.
In 1964 the Colt Firearms Company started noticing the marketing dollars for swag all going to the ballclub and gave notice that things would have to change. Roy Hofheinz used this as his opportunity to change the name of the team from the Colt .45s, which he never liked to the Astros. Originally, Hofheinz had promoted the name "Stars" but was overruled.
Legend has it that Hofheinz had all of the Colt .45s memorabilia destroyed.
I do remember when I was very young, the team being nominally referred to as the "Colts" as often as the "Colt .45s". I have a vague memory of asking my dad about the discrepancy.