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.