The phrase 'bells and whistles' - used to refer to unnecessary but perhaps fun things - is a surprisingly new one. It also seems to have come to prominence in the early-ish computing world - the earliest example of the phrase in the Oxford English Dictionary comes from 1977, in Byte magazine, which refers to how "this simple circuit..even has a few outputs that can be used to provide user defined functions, such as enabling external devices or turning on bells and whistles."

The OED also claims that the term originally comes from the practice of large organs having bells and whistles - and some large organs certainly did have bells and whistles, most notably in the silent film era when they were expected to provide sound effects to what was happening on screen.

However, previous to the mention of 'bells and whistles' in Byte magazine, the only uses of the phrase I can find come from discussions of locomotives (e.g., in this 1970s discussion of reductions of the noise emitted by American trains) rather than organs. In 1983, a general testifying to the US Congress uses the term 'bells and whistles' when talking about an air defense gun, leading a congressman to ask them what the phrase means. Given that the congressman doesn't know the meaning of the term, and that, I think, a US general in 1983 probably isn't up on hacker slang, but might be up on engineering slang.

So I think it's perhaps likely that the term came from locomotive engineering, rather than musical organs. Trains have loud horns, and so bells and whistles are probably superfluous? But they were clearly present on some trains judging by what turns up in Google nGrams. And if 'bells and whistles' is originally (military?) engineering slang, I see the phrase being derived from train design rather than organ design.