I personally don’t think [name_m]Shepherd[/name_m] is “too out there” at all.It’s kind of in the same category as names like [name_m]Hunter[/name_m], [name_m]Archer[/name_m], [name_m]Sawyer[/name_m], etc. From an Australian perspective, it does read quite American to me, and I’d probably associate it with the [name_m]Southern[/name_m] US and possibly a more religious context just because of the word itself, but that’s more about cultural association than anything “wrong” with the name.
I also don’t think it’s too much to worry about the sibling name matching stylistically. [name_f]Stella[/name_f] and [name_f]Elowen[/name_f] do feel quite different in vibe to [name_m]Shepherd[/name_m], but that’s totally fine. Personally I’d lean [name_f]Elowen[/name_f] just because I prefer it, and I like the idea that each child has their own initials.
I also think the meaning behind it for you makes a lot of sense, especially as a subtle honour name - that kind of personal significance tends to matter way more long-term than how “common” it is. So I say go for it!