I cannot speak directly to how Jansson worked, but I have done hand work like this for posters in the 1980s and from the looks of the images in the search you shared, then the answer is these were "hand separated." However, rather than break up a single artwork using color filters into constituent parts, these would have been submitted as n- separate drawings (one for each color) with each having identical registration marks.
I would have started with a single artwork and then laid tracing paper of the sort an animator might use over that work so the registration marks align. I would then trace out sections I want for an individual color and work in any details etc. This would be in black ink, but the sheet would be marked "color 3" or whatever with an indexed color chart corresponding to what the ink will be. Repeat for each color. This might be iterative and the original drawing I used might not even be part of the submitted color series. When these drawings are all overlaid and registered against a lightbox, one might see very little light shine through. In the case of Jansson's work, it might have the effect of "scratch art."
Some color might overprint another, but the inks themselves would generally be solid (no halftones). To get tints or tones an artist might hand-stipple or they might use pre-made halftone screen sheets from someone like Letraset cut to size, pasted to the drawing, and sometimes modified or tweaked using "white out." I do not see halftones in the items in your search by the way.
The "gaps" are mostly a stylistic choice but they are there to avoid unwanted overprint; because the hand-registration process between individual artworks is imprecise; and because registration on press (especially if serially printing arbitrary colors on a 1-color press) using older equipment with poor tolerances is difficult. Many illustrations of this type use the weaknesses in the technology chain as a strength.
There may be discussion of Jansson's process not in English, but there is no reason the process I mention above couldn't have been done by a pre-press illustrator using Jansson's work as the base art.