As another example, Clones use a minimap that's only shown while holding down a hotkey. It is shown as an overlay that's centered on the screen and actually takes up a good portion of it (so it basically obscures a good chunk of your view of the level itself while shown, though there might've been some translucency effects, I don't remember). So it's able to use a much larger portion of screen real estate and is not forced to fit into a particular fixed-size box.
It's not exactly the best system, but I think any minimap that needs to work with varying level area dimensions will probably have to be some form of overlay that's shown and hidden on demand, at least to be functionally complete. It is of note that when vertical scrolling was introduced starting in Lemmings 2, that was the version where they also started removing the minimap. So probably DMA hit the same design difficulties, and with the technologies of the time, implementing an overlay may not even be technically feasible in some systems they'd want to target the game for. And as far as I can remember, minimaps never made a comeback in any subsequent official games of the series.
And to be fair, even if right-click scrolling is as fast as a minimap in terms of scrolling, it does require you to have a rough idea in your head where you need to go in relation to the full span of the level area, while with the minimap it's more like visual targeting. Being able to see lemmings outside of the current view area might also be useful, but I think in most cases, the minimap doesn't really show enough details to warn you effectively of lemmings-about-to-get-into-trouble sufficiently ahead of time (though arguably a few tweaks can improve on this front, such as flashing the lemmings that have just changed their actions, like finishing building or bashing or starting to fall).