If I were doing this, I would do the 6 page method you mentioned, export the PDF as 2 pages to make the printer happy,
and then for the web layout… I guess it depends on how much time you have and how much experience you have doing web design.
No time at all = rearrange 6 pages logically in the order you’d want the viewer to see them,
left to right and then top to bottom, export with no changes at all. 3 panels fitting the width
of the display, then 3 more after they scroll down.
A little time = make a new ID file and copy-paste the contents to a slightly different layout
that is more web-friendly… for example the front cover of a brochure would be tall and thin,
buit the header of a web page would typically be wide enough to fit the screen width.
So you’d basically copy and paste the contents of 3 panels onto one landscape page
and shuffle items until they look good.
Lots of time / paid web desiger = maybe do a nice interactive online brochure
where the user can click and open up 3D-looking “folds” as if they were handling
an actual printed brochure. Then your layout doesn’t change, you just get a 6 page
PDF to your web guy and let them hassle with the rest.