@manton is working on bringing those pages closer to how user-created pages function. Don’t know for sure, but I think you will get that checkbox when he’s done.
Until then, this custom CSS will remove the pages from your navigation:
nav a[href="/archive/"],
nav a[href="/photos/"],
nav a[href="/replies/"] {
display:none;
}
Add the snippet to your blog by navigating to Design → Edit CSS.