Thank you!
My feeling on (1) is "no" - I think that in classic D&D there is an assumption that alignment is to some extent manifest (through behaviour, choice of holy symbol, choice of companions, etc).
Agreed, especially with regards to behavior and, perhaps, general demeanor. For me, it hearkens back to the medieval concept of the unity of goodness and beauty, and of course its opposite, the unity of evil and ugliness, and I for one like my D&D to have a medieval flavor. If the alignment of the person manifests itself outwardly, however, and that is what the reaction is in regard to, then what is to prevent someone who is skilled in such things from counterfeiting a "false" alignment? I suppose to successfully pull off such a deception some speaking would be required as I would expect for most Charisma-based abilities. But, yes, I think that an aligned creature could be expected to react to the difference in alignment between itself and another without anyone uttering a word.
On the other hand, the presence of the Know Alignment spell might suggest otherwise. So my feeling of "no" is perhaps contradicted by that spell.
I think its important to keep in mind that to have a reaction to either a difference in alignment or to someone's alignment itself in no way requires the reactor to
know what the particular alignment is. I think of it in terms of getting a good or a bad feeling about a person. Of course, players themselves get these kinds of feelings about creatures their characters are having encounters with because of the way the DM describes and/or role-plays them.
The way I regard alignment in my campaigns is that it's a meta-game concept. People in the game-world don't have specific names for alignments and certainly don't use the terms we do, which are merely a convenient way for those playing the game to categorize the views, beliefs, and attitudes of characters and monsters about their relationship to the rest of the world. It would mean nothing to anyone in the game-world to identify someone as one particular alignment or another. And yet we have this spell that seems to allow a cleric to receive meta-game knowledge. I would suggest that the caster of Know Alignment is actually gleaning complex information about the target which the DM can most easily summarize by revealing the target's alignment to the caster's
player. It isn't necessary to assume that such information is available to the reacting party in an encounter, but it may be that the same manifestation of alignment upon which the spell operates, i.e. the creature's
aura, may be that to which at least some of the reaction is in response to. In which case, it might be even more difficult to fake your alignment.
My feeling on (2) is "yes" - creatures of no intelligence or animal intelligence probably shouldn't be affected by alignment, at least if they are themselves neutral.
I was thinking in terms of fifth edition here. Of course in first edition there are no
unaligned creatures, but you seem to have gotten my point anyway. I should have said neutral. Obviously creatures who in fifth edition have been identified as unaligned could not react to any
difference in alignment, but since alignment is the relationship that one has with the rest of the world, it is possible that an unaligned creature would react to the alignment of a person able to communicate with it, manifested either through words, manners, or the person's aura. A good-aligned person may give the creature a sense that its life is valued, whereas a chaotic evil person may produce the opposite response even though the creature itself has no particular alignment of its own. This is why evil creatures still have a negative reaction to a chaotic evil character.
My feeling on (3) is "not without difficulty" - otherwise the Assassin ability to disguise, and to learn alignment tongues, becomes even more boutique than it already is!
I'm glad you mentioned alignment tongues. In his discussion of alignment languages on page 24 of the DMG, EGG warns strongly against the use of alignment tongues for the purpose of initial contact, and that revealing one's alignment by such means would be perceived as a serious faux pas, even by creatures of the same alignment. It occurred to me upon reading this passage that alignment tongues weren't really put into the game for the player's to reveal their alignments, but rather for the DM to reveal the alignments of NPCs to the players when it was important for the players to trust the NPCs were acting in good faith. I suppose that the Assassin's ability to learn the tongues of other alignments is a way of turning this dynamic around, allowing the Assassin to gain trust, from an NPC or another player's character, where none should exist.