Now I had some time to work on the shelter-issue again.
Long story short: I'm giving up on this now, but not because I didn't find a solution, but because the key I'm interested in is used so inconsistently, it would clutter my maps.
Long story long:
Because I wasn't sure, what you meant with
to edit benjamins source to prevent the deletion of the filtered input file and check if shelter=yes is in the filtered file
or which file to check exactly, I tried '.\wahooMapsCreatorData\_tiles\germany\filtered.o5m' first. With osmfilter I could find the following keys:
160 shelter:check_date
1 shelter:left
1 shelter:name
2 shelter: perator
1 shelter:ref
2 shelter:register
1 shelter:register:note
1 shelter:style
9 shelter_shape
1 shelter_size
63850 shelter_type
1 shelter_type_1
There is no "shelter" without additional ":" or "_". So if I'm not mistaken a node or way with just the key "shelter=yes" would not be included in the file, right?
If I compare this with other keys, e.g. waterway, the other keys are always available in a pure form, without additional ":" or "_". And unsurprisingly, they have the highest count:
1641366 waterway
1 waterway:-2021
4904 waterway:category
1 waterway:de
5 waterway:distance
1 waterway:hazard
119 waterway:kilometer
5 waterway:lock:height
5 waterway:lock:length
1 waterway:lock: phone
1 waterway:lock:width
7 waterway:maxheight
145 waterway:maxspeed
7 waterway:maxspeed:motorboat
1 waterway:milestone
4 waterway:mindepth
2 waterway: position
619 waterway:sign
6 waterway:type
6 waterway:ukw_channel
3 waterway:vehicle
1 waterway:vhf_channel
2 waterway_1
2 waterway_category: DE-NI
333 waterway_category:NDS
Moving forward I wanted to test if I could include nodes or ways with the key "shelter_type=*" in my map files and display them in my theme. Using overpass I was looking for such an object in my vicinity so I could check it in the map tile I normally use to build my theme. I found some objects nearby, but all of them would have been in my theme anyway because they also contained the key "amenity=shelter".
This made me think about the key "shelter=yes" once again. Using overpass once more I checked how the key is used in my vicinity. And what I found made me drop the idea: often times the key "shelter=yes" is used multiple times per single bus stop because it is used on a way in addition to "public_transport=platform", on a node in addition to "public_transport=stop_position" and on top of that on a node with the key "public_transport=platform", too. So in the worst case my theme would display three shelter-icons when there's just one shelter in reality.