Well, the GM intends to roll on the encounter table. So they're not uninentional in that sense. But they are, in a certain sense, spontaneous.The part about the random encounter is that it is by definition unintentional.
You are making assumptions here which I think are not universally, perhaps not even widely, true.That's the purpose the mechanic serves: you roll it when you want to create an encounter without much context.
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a random encounter has no agenda determined for it until it enters play (where the agenda is determined then by its immediate context).
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"I meet an assassin" is a random encounter and it triggers questions (Who is this assassin? Why are they here? What are they doing?). "The assassin comes to kill the PC's" is, without other context, not a random encounter, it is a planned encounter
For instance, the random encounter or "wandering monster" mechanics isn't used just to create an encounter without much context. In classic, Gygaxian, D&D play it is also used as a pacing technique and a punishment-for-poor-play technique (ie you encounter wanderers if you waste time and/or make a lot of noise).
A random encounter certainly has not agenda until it enters play - although for some playstyles that is true also for many non-random encounters: Eg, in my 4e version of G2 I have placed fomorian envoys in the duneon rooms 6 and 7 (replacing the ogre magi and cloud giant in the original). The PCs encountered the fomorians (or, in fact, their cycopes guards, replacing the original's ogres in room 9) at the end of the last session. I decided on a loose agenda for the fomorians while writing up some stats last night - I will settle on the details, if I need to, during the actual encounter between the PCs and the fomorians. (If that encounter is mostly combat, then I probably won't need any more details!)
But the fact that a monster or NPC's agenda is not authored until it enters play doesn't mean that that agenda has no depth beyond the immediate context. For instance, to play on an example given (as best I recall) by Moldvay in chapter 8 of the Basic rulebook, if there are giant ferrets in the dungeon, and I role a random encounter with a trader, I might decide that the trader is there hunting ferrets. If this is the second trader encounter I've rolled, and the players killed the last group of traders, I might decide that this trader is a friend of the earlier group trying to find out what happened to them, or perhaps a rival, even an envoy from a rival trading clan, depending on what seems interesting and fun. (In B/X, at least, the reaction roll can also be part of this - why was the trader hostile? because he recognised his friends' mule, now taken by the party; why was the trader neutral? because he is an envoy from another clan; why was the trader friendly? because he was looking for help in tracking down giant ferrets.)
There has never been any rule, or even suggestion, that I'm aware of, that random encounters are not to be connected into the deeper backstroy and unfolding events of the game. An assassin encounter raises no special issues in this respect that I can see. Is the assassin here to assassinate the PCs? Or on a mission to assassinate someone else and seeking to gain information from the PCs? Or just passing the time between paying jobs? Or even in the market for a hit, and regarding the PCs as potential clients? Any of these strike me as feasible - which one can be determined using the same general processes as are used for any other random encounter.