Lets have a look in my part of chartered space, District 268. There are 9 systems with Class E ports.Generally speaking Class E Starports are in the frontier and very low TL which also means the atmosphere is breathable. And you don’t need an Airlock to depressurize your cargo bay to unload it most ships cargo bays are separate from the rest of the ship. The Marava has two cargo air locks and the Hero, Beowulf and Subsidized Merch all have separate cargo hold so they don’t need an air lock. I would say the latter 3 are good examples of why Airlocks are generally considered a waste of space on a trader.
Milagro requires a Vacc Suit
Datrillian requires a filter respirator
Talos, and 567-908 require a respirator
Dawnworld is dense but breathable
Faldor requires a filter
Flexos and Noctol require an air supply
Judice has a corrosive atmosphere and requires a Vacc Suit (likely a HEV Suit).
So the vast majority of class E ports require some sort of airlock to avoid damage, contamination or simply bleeding out the air supply. Only one is breathable without extra gear and even then you might suffer over pressure effects if you were not careful.
By separate hold you mean on some versions of the deck plans a hatch has been arbitrarily drawn. Which could be added to any ship at no cost since it is just an icon. But if you want to expose the entire hold of your subbie to who knows what and spend the time depressurising and repressurising it (so you can have a shirt sleeve atmosphere that some people seem to think should be normal) there is nothing saying you can or you cant.
Whether you think it is a good idea or not depends on how you intend to use your ship. You get one airlock free for every 100 tons or part thereof (which take up no space apparently since it isn't listed against their capacity). Extra ones are a minimum 2 ton but there is no stipulation on how big a cargo one needs to be and there no reason that you cannot make it up from the free ones so a 400 Dton ship could have 1 passenger airlock and up to 3 designated as cargo (or presumably that could be replaced by one big one that is three times the size). Even if you paid extra for a cargo airlock what does a 10 Dton lock mean. It takes up 10 DTon, but can it hold 10DTon of cargo in the lock. If so you aren't really giving up the space for it as you can always store some cargo in the lock itself*. You have to pay a little for it, but that seems a small price to play for the flexibility.
Seems a lot of fuss over something that is largely glossed over in the rules.
* which is functionally the same as a cargo bay with cargo hatches - as this is also an airlock according to HG p25