Yes, I didn't notice that, I should have tested it more thoroughly!

Make works best when there's a simple relation between target filename and the dependency filenames, and when the output filenames are known ahead of time (or are easily derived from a list of inputs).

You can use Make to achieve what you want though, even when the relations are complex. The idiomatic pattern is to dynamically create your dependency lists and include them at runtime. Make supports this as a first-class feature and will handle re-evaluating any rules that are changed every time an included Makefile is (re-)generated.

For example:

SOURCE := $(wildcard source/*.md)
SDEPS := $(SOURCE:.md=.d)

include all.d
include ${SDEPS}

all.d: ${SDEPS}
	sed -i "s/^/all: /" all.d

${SDEPS}: %.d: %.md 
	DEST="destination/$$(basename $< | sed -E 's/^([0-9]{4})-([0-9]{2})-([0-9]{2})-(.*)\.md$$/\1\/\2\/\3\/\4.md/')"; \
	printf "%s: $<\n" $${DEST} >$@; \
	printf "%s " $${DEST} >>all.d

%.md:
	mkdir -p $(dir $@)
	/bin/bash ./myscript.sh $< >$@

(I've tested this one and it seems to work)

But if you want to avoid any complex use of Make then you can push a lot of the logic into your script and then just create a timestamp file for each input as a dummy output to represent the fact that the script was run on each input. eg.

SOURCE := $(wildcard source/*.md)
SOURCE_TS := $(SOURCE:.md=.ts)

all: ${SOURCE_TS}

%.ts: %.md
	/bin/bash ./myscript.sh $<
	touch $@

This is a much simpler Makefile, but now you need to create the output filename, make the output directory and redirect the script output inside the script itself. The other drawback is that it's harder to use the output file as an input to another rule. You can use the timestamp file as an input but you won't have the actual filename available to send to a command without some more scripting.