Can you look at one of those CD's you burned?
And do a list from the shell?
Just a list of some random dir that has some files in it.
And paste the list here for me?
When I did it all my files came up as
filename r-ed----
This means when you restore such a backup, tons of software won't run anymore. I think you never restored any of these backups you made or you would have noticed the problem, as it is very annoying to have it happen.
Well, I have restored them many times. I've never had a problem. The RWED flags are all enabled. All directory structures (even deep ones) are preserved.
I've done this many times since about 2002 until today.
As per your request, I pulled an old backup CD-R I did in 2007. I "LIST"ed a directory on that disk. Here is a screenshot (click it to make it bigger):

As you can see, all the RWED permission flags are all enabled.
The only unusual thing I've noticed is that sometimes the file creation dates look wrong in the listing (both on the Amiga side and when the CD is viewed in Windows). For instance, some drawers have the date "FUTURE" and others show a Dec-17-2012 date even when the disc was burned long before that. But the files are always good and all directory structures are preserved.
Here is one where the dates look wierd:

I did this for about eight years while I owned a real hardware Amiga, then after 2008 when I switched to WinUAE I continue to back up my Amiga partitions to a CD-R this way.
To restore from one of these CDs is very easy, just copy the root directory to the Amiga partition you want the whole thing to be restored to.
As I said, I am using MakeCD.