Bones already work much in the way you describe.
Look at this femur for example: https://www.google.com/search?q=femur+cross+section&oq=femur+cross+section&aqs=chrome..69i57j0l2j0i22i30l2.10425j0j7&client=ms-android-samsung&sourceid=chrome-mobile&ie=UTF-8#imgrc=dIRLPBbsIdAJhM
You have an outer "shell" that has some thickness. Near the center it becomes hollowhollow*. At the outer ends more forces are located in different directions and these are supported by the criss-crossing of small bone supports. The more forces are located there the more dense these bone supports get.
Your honeycomb structure would actually give weaker bones in that respect. You would have honeycomb in the center where its not necessary and would add unnecesary weight, at the top it would need to be smaller and denser honeycombs to support the extra forces or risk breaking the bone.
You are probably better off using different materials. Special Spidersilks to reduce the weight of skin, tendons, bones and other facia in the body without sacrificing strength. The drawback being making it harder to heal when it gets damaged and requiring a lot of clever bodily designs to migrate spidersilk strands through the body.
Other options are Graphene reinforcements. While complete Graphene structures is likely too hard the addition of Carbon Nanotubes helps strengthen materials, allowing you to keep them lighter. Many processes of the creation of Graphene can already be done through biological processes such as certain bacteria. It would not be too much of a stretch to say your bio-engineered creature can do this and add it to its bodily structures.
*although partially filled up with bone marrow it always amazes me how people make hollow bones on birds and raptors significant, while most living beings essentially do the same.