If I want to remove existing Fossil commands or webpages to create a customised version of Fossil, can I simply delete the C code page for the command or webpage, recompile Fossil, and expect it to not break anything else?

You don't need to remove the code, just the "COMMAND:" or "WEBPAGE:" marker from the comments above the code (or just add an "x" to the start of each, or similar). That would work for most commands, but a small number of them call each other.

For web pages it's not quite that simple: removing pages does not stop fossil from generating links to those pages at random places around the UI. If you don't find and remove all such links, you risk a lot of dead links in the UI.