Hi Kiyoshi,
I really haven't tested the folder sub sites feature under Mono myself yet.
About the menu icons though, part of the problem is that Mono hasn't yet implemented support for CSS Control Adapters so the ASP.NET Menu and TreeView are rendering as nested tables instead of as ul and li elements. In the control adapter I'v put in handling to correctly resolve the image urls when using sub folder sites but that code is not runnning because its using the ordinary control on mono instead of the adapted control. If you view the source of the page on your site vs the same code running on windows, you will see clearly the difference in the rendering of the menu. I've seen some commits going into Mono svn that lead me to think they are working on support for the adapters so hopefully this will be fixed in future version of Mono.
Note that when using the folder subsites I have to maintain the subsite folder in all navigation urls but image urls still need to be relative to the root site. Apparently there is some difference in Mono that is not working correctly.
I might be able to get it working correctly in Mono if I play around with it but ideally the support for adapted controls will fix it for us and is a much better way to render a menu.
In the meantime you could consider using the host name sub sites instead of folders, it should work better because there is no virtual folder to deal with and everything already has the correct relative path.
Or if working with source code in MonoDevelop you may be able to fix this yourself by modifying Controls/SiteMenu.ascx.cs
Hope it helps,
Joe