During the second chapter (While you're disguised as nazi officer.) there seems to be some censorship.

The other soldiers don't do their little Hitler salute like they did in the original release and a few lines during the conversation between those two warehouse workers near the beginning are missing, one guy's just moving his lips while remaining completly silent but the other one still responds.

It wasn't like that in the original release, so what's up with that?

Best to ask GOG support about this. Sometimes they can investigate and update their installers with the uncensored version (such as they did when I pointed out the censored MDK).

Alright, I just did.

Yes, I have noticed that too, maybe the first release version was U.S. version of the game and this one on GOG is EU...I do not know if this theory is right but the game has loss some of its atmosphere by removing this content, nevertheless, this is a game form German Nazi war era...

Are you serious? They censored this game?

Also one of the final missions is censored - Die Sturmgewehr, because you have disguise there too.

Fuck I bought it a minute ago....damn!

Want my money back!

Goddamn GOG WTF?!?!
Please release an uncensored version!!!

I'm not too surprised by this, in a lot of countries anything associated with nazism is forbidden, hence there are no swastika's on german aircraft in IL-2.
Gog probably did this to prevent a boycot in those countries.

I just got the game yesterday too but if GoG did censor some things to prevent a boybott, then they were pretty selective about it. In the opening sequence of the first mission, you could still see banners with the swastikas on them and normally it's this kind of thing that gets censored. I seriously hope what the OP pointed out was just a bug and nothing more.

EDIT: I just got to the part you mentioned in your post but I didn't seem to be having any problems. As soon as I entered the mission, I holstered my weapon and as soon as you pick up the officers uniform and level 1 papers, two troopers will enter the locker room talking in German. They say a few lines to each other but if you just stand there watching them finish the dialog, they still did the salute along with a hearty "seig heil". After trashing the prototype and heading through a door, there will be three troopers who all salute and say "seig heil". I don't seem to be having any problems here.

However. I still find it strange how I'm having no trouble with missing dialog or salutes but the swastika insignia seems to be missing from all enemy soldier uniforms. The officer's uniform seems so bare without the red swastika armbands, were they missing in the CD version too? The cross is still on the uniform and the eagle on the officers hat are there, just no swastika. Troopers have no insignia whatsoever on their uniforms which I thought was strange. If they went out their way to censor the swastika on the uniforms then why are there still swastikas on the banners?

This is either bad uniform design by the games devs, a bug, or some of the sloppiest censorship I have ever seen in a game.

I just did comparison between old CD version (patched to 1.11) and GOG version and there is, indeed, small differences in files. I put old files in pk3 file that you must put in "main" dir. I don't know is it bugfix or censorship. As far as I can tell it, they just changed full "Sieg Heil" salute in ordinary "Heil".

You can see differences yourself if you load my save, and wait that soldiers in first room salute you. Try with and without my pk3 file.

There were also some files missing from sound dir, and you can download them here: sound.rar. Maybe files are unused in GOG version, and removed because of that.

The soldiers say both "Sieg Heil" and "Heil" in the Gog version, nothing was censored there. In the CD version, were there any swastikas on the uniforms? That seems to be the only thing censored. The missing files thing is strange though. Hope a gog staff member will see this thread and give us the scoop on what's going on here.

I did notice something a bit strange in the third mission after Omaha beach were you have to defend the house. After the house defense part and your jeep get's blown up and you move outside the yard, your two allies will talk but them suddenly stop but their lips are still moving. I'll reload that area again when I have a bit of time as it might have just been a glitch but maybe the speech files were missing as you said (though what could be censored there I have no idea). There seem to see quite a few glitches in this game after all. On the Omaha beach landing mission when you and 3 guys make it to the bunker wall, after two of the guys get shot running across and you have to run across, sometimes the officer guy lays down covering fire in the wrong direction.

I checked all the files and everything is the same in both, GOG and CD version, except small change in salute of german soldiers when you are in disguise and few missing sound files I mentioned above. I don't know are these sound files ever used, but this change in salute may be just a bugfix.
In example:
CD-Version script: GOG-Version script:

The armbands are still there. They are only on elite sentries (the guys in black that check your papers. See attachment - pic taken from the GOG version today.)
I don't remember any other types of soldiers wearing them in the CD version, but I'll have to check sometime to make sure.

As for the missing salute - this is just a guess - it could have something to do with Spearhead being installed. I recall back when it first came out, I installed the Spearhead expansion, and later noticed some small inconsistencies with the base game. I can't remember specifically what they were, though.
Of course, this is just a guess, and I have a bit of a shitty memory.