I’m torn about them. On the one hand they free up the combat design to be as wildly different from the exploration as it wants. Which can result in really creative stuff. Favorite examples are Undertale, MegaMan Battle Network series, and Tales series.
But on the other they interrupt the flow of exploration, the music, you forget where you were by the end of combat and they can be very annoying if they happen to be common or just as you’re about to leave an area. The consolation prize of growing stronger with every battle only helps so much.
Random encounters tend to be trash mobs, and I hate trash mobs. I know even in the late 90s, there were some prehistoric internet memes about FF7, and having just played it recently, I remember why. There were so many of them. You’d easily forget where you were going and what you were doing because you’d be interrupted by random encounter trash mobs every couple of seconds. They weren’t too hard, so you didn’t have to think very much to get through them, which made them uninteresting, and they also, like you said, just kind of screwed with the flow of the game. So generally, I don’t like them.
The annoying thing is, the problem with this from a design perspective was well known and there were already some efforts to improve upon matters as early as the SNES era. Both Chrono Trigger and Earthbound leap to mind. It’s just that following this, most developers forgot to learn a lesson from these for another decade or two.
In Earthbound, all non-story, non-boss encounters are visible on the overworld and you can either:
In Chrono Trigger, most trivial encounters can be avoided, with some scripted exceptions that always initiate when you cross a certain area presumably to prevent players from completely avoiding all combat entirely and subsequently getting their asses stomped by the bosses. Chrono Trigger’s overworld map also features no random encounters whatsoever. You can wander the world freely and will only encounter monsters if you actually enter a location.
I harp on this a lot, but only because it’s true. Despite its faults, some of which it definitely has, Chrono Trigger had some incredible design innovations and was easily the high water mark for JRPG design not only for its time, but even compared to subsequent games for a long time – maybe even still to this day.
Etc.
Apparently the Chrono Trigger devs originally planned to give the player even more freedom but several additional concepts such as being able to freely position your fighters on the field were cut due to time constraints and not being able to figure out a sufficiently elegant way to do it on the SNES hardware and controller.
It’s worth noting too that trash mobs aren’t limited to random encounters. Baldur’s Gate 1 and 2 are littered with trash mobs, and none of them are random except for maybe traversing between towns.