From my experience in the US Navy:
Enlisted people below the rank of Chief Petty Officer aren’t addressed as ‘Mr.,’ ‘Miss’ or ‘Ms.,’ but traditionally with their last name alone. In my personal experience – which was all on small, linformal shore commands with a lot of civil service civilians working with us – I was usually called by my first name. According to my husband, though, on ships, as recently as two years ago (when he retired) enlisted people are still called by surnames alone, at least by most people who outrank them. In my father’s day, enlisted people used surnames alone even among themselves, BTW. This has largely changed – among themselves enlisted people use first names. And, according to my husband, some younger officers seem to prefer first names for the enlisted people working for them. My husband, and most other traditional types, still prefer the surname-only usage. And, in any case, ‘Mr.,’ ‘Miss’ or ‘Ms.’ would never be used.
Chief Petty Officers (E-7 - E-9) are always called ‘Chief,’ ‘Senior Chief’ or ‘Master Chief,’ either with the last name or alone. Sometimes Senior or Master Chief is shortened to ‘Senior’ or ‘Master’ alone, but never with the last name – you might hear, “Hey, Senior…” or Hey, Senior Chief Jones…" but never “Hey, Senior Jones…” You never call a Chief, ‘Mr.,’ ‘Miss’ or ‘Ms.,’ nor Sir or Ma’am – not unless you like to be chewed out. Typically, if you so misaddress a Chief you will be told either, “I’m not a ‘Sir’ – I work for a living!” or “I’m not a ‘Ma’am’ – my parents were married!”
Officers: Junior officers are usually addressed as ‘Mr.,’ ‘Miss’ or ‘Ms.’ or Sir or Ma’am. I worked with a number of female junior officers and used ‘Ms.’ or ‘Miss’ at their preference – I suppose ‘Mrs.’ would have been equally correct, but I never knew one who wanted to be called that. ‘Ms.’ was the most common preference although I knew a few who went by ‘Miss.’ Occasionally ‘Mister’ was used alone for a male Junior Officer, but I never heard ‘Miss’ or ‘Ms.’ used alone. It just sounds funny, I guess. If we were in a hurry, we’d just say ‘Ma’am.’
Senior officers: Their rank (alone or with the last name) or Sir or Ma’am.
Using ‘Mr.’ as an honorific for women: Never in real life. The honorific for women is either ‘Miss,’ ‘Mrs.’ or ‘Ms.’ The notion that the female honorific isn’t quite good enough and should be replaced by the male is a bit offensive to me.