I'm working on a theme that doesn't respect most of the default theme options, like rows/columns, thumb size, that sort of thing. I have a very good reason for that, don't worry (and I'm happy to take on the argument, but perhaps not here & now).

So I want to remove or hide them in the options for my theme, as they will only be confusing. They won't do anything, and I certainly don't want to raise false expectations from people who might use my theme, when I release it.

You cannot remove or hide options but you can disable them. See the Zenpage theme for an example.

It's perfectly fine to not cover most options. Almost all themes I create for sites uses custom sizes on the theme instead of any options. And the concept of rows/columns is stone age and to be removed in the future anyway.

Sounds good, I'll check it out.
If it's common to ignore options, then I suppose it shouldn't be as confusing to users as I anticipated. Still a bit, but not as much :)

If it's common to ignore options, then I suppose it shouldn't be as confusing to users as I anticipated. Still a bit, but not as much

What is confusing? That they can't be hidden completely? That is planned but not possible with the current code base of option handling. That's being reworked for the major release although it has less priority.

The confusing part is when there's an option that doesn't do anything by design (of the theme).

It's confusing to a user, mind you. Not to me.

Yes, I agree on this and it's on the list for the backend rework later as option handling needs to be changed.

However this only applies to some standard options and not for custom options which of course only appear when you add them ;)