The non-remastered version is missing from the store.

Does the so-called HD version from Emberheart include the DOS game as a bonus?

Humble_B is absolutely correct. The original DOS Secret Agent and Crystal Caves are no longer available for purchase on GOG. DOS version of Crystal Caves is available as an optional extra if you purchase Crystal Caves HD, but Secret Agent HD has no extras, so it's DOS version is simply no longer available on GOG. If you did purchase these games for DOS when they were available, the originals are still in your GOG library for download, even if you later purchased the HD remakes as well.

Bizarrely, 3D Realms isn't selling most of their games directly through their website either. The only way to purchase the DOS version of Secret Agent, it seems, is via Steam.

Just in case anyone isn't aware, GOG has both versions.

https://www.gog.com/en/game/secret_agent
https://www.gog.com/en/game/secret_agent_hd