Title says it all. B-wings definitely get shot being an Alliance creation. Probably A-wings get shot, I'm not sure how long they've been around or if they are specifically Rebellion. What do you have?

B-Wings were used by pirates in Heir to the Jedi , weeks after ANH.

A-Wings have now been around since ROTS or so (Bail has a fleet of them, and uses it in the Ahsoka novel.

Y-Wings were heavily used by the Republic before the Empire started mothballing and then scrapping them - during that interim era I could see them being used by planetary defence fleets.

X-Wing probably see the least "outside of Rebellion" use - that said, in the EU, CorSec used them, even when Corellia was loyal to the Empire.

So, I could see (at least early in the Civil War) Imperials being cautious rather than aggressive when confronted with apparently nonhostile "wing" craft - especially if broadcasting non-Rebel identification and claiming to belong to a planet's militia.

Y Wings were sold as planetary defense ships until the empire stopped Koensayr from doing so...I don´t
​know if they marked them as military and forbid them afterwards, so maybe they are still ok to own?
​Citadel Class Freighters are basically Combat ships sold as freighters...
​Same with the 4R3 light assault transport from dangerous Covenants..
​A7 hunter interceptor is sold as planetary defense and mercenary groups, although strictly regulated by the empire.
The Starships from Suns of Fortune are propably ok bc Corellia has kept a certain degree of independece from the empire.

I guess any ships who doesn't belong to the rebellion or known pirate groups is safe from immediate attack.

It seems that the great criminal groups (Hutts, Black Sun, Tyber Zahn etc..) can have private fleets without any "imperial entanglements". Normally all the planetary defense forces ships are allowed too. So the empire is quite lenient in that regard (of course they usually have the most badass ships around so they can afford that). So any B-Wing, A-wing or X-wing are attacked on sight, unless they have a very very solid cover story or justification.

In general the galaxy seems quite similar to the high seas in the 1700-1800 hundreds: a dangerous and lawless enough place that most ships are expected to be armed to defend themselves, so the empire won't immediately shoot all warships it finds. Look at the latest Rebels episode: an imperial cruisers spots a ships which turns out to be the Ghost, a known rebel ship so they attack it. If the ship had showed up as the "Verpine Shadow" they wouldn't have attacked....but they might have investigated further.

Any of em? None of em? It really really really really depends on the situation.

A-wings, Y-wings, and literally dozens, if not hundreds of other starfighters are, or were, available on the open market in the Star Wars universe for years. Furthermore military hardware in nongovernmental hands isn't all that uncommon (at least in the mid-outer rim). Piracy and related activity is pretty common, and civilian craft are allowed to fit (and regularly come stock with) not unimpressive weapons packages. And then there's the active Bounty Hunter and Merc Markets...

So when put in that lens, you can see that, in most cases, the Empire probably wouldn't just automatically attack any fighter on-sight. That flight of Y-wings might be Rebels, or it might be a perfectly legal registered security company, or planetary defense force, or diplomatic guard, or corporate convoy escort or... Remember, IFFs work in Star Wars too, so actual military combat craft with the rebellion probably mount their own IFF that broadcast as Rebellion just to keep things clear and avoid the appearance of war crimes.

I think Admiral Ozzel, despite his incompetence, makes a good illustration in ESB. When they first find Echo base, he totally blows it off "There are so many uncharted settlements...". Even the fact they are possibly Pirates or Smugglers, both "bad" things int he eyes of the Empire, doesn't bother him enough to think even a single cruiser needs to check it out. Put simply, there's so much stuff in the galaxy that the Empire simply can't assume that every non-Imperial combat ship they come across is hostile... even models of craft that are just "suspicious" won't necessarily attract that much attention if all they otherwise look on the level.