Generally speaking, it's fine to put the solutions in their own directories. With PowerStore though, for many people, that would constitute their main website, so the files and folders for PowerStore are often put directly in to the site's root directory.
As powerstore already comprises other WebAssist software (CMS, HTML Edtor), it does make sense for this to be in the root directory, because if you choose to customise (for instance) HTML Editor , then this can easily be done without having to create a new site definition in DreamWeaver with the Powerstore sub-directory as the delegated local and remote site root directories. [If you don't do this, then making changes to the HTML Editor configuration will create a whole new HTMLEditor directory in your actual site root, seperate from the existing one in the PowerCMS folder. This can get confusing!]
But your site may be a portal for more than one Store, in which case each would need to be in its own sub directory. (Or your store may be just a small part of a larger site, and just to keep your root directory files tidy you can put it in its own folder).
PowerCMS (I believe) should be in its own directory anyway, and also PowerGallery. For the contact Form Solution Pack, I always create that in it's own directory, but when it's set up, I 'Save as' the contactus.php and thankyou.php in to my site root directory. so that my contact page and thankyou page are in the same folder as my other main pages (and are likely to be using my site template).
Seperate directories keeps your site structure 'cleaner' and (I think) more logical.
No firm rules, but your point about solutions with similar sub-directories is valid (for now) - but I believe WA are taking this into account with new releases and upgrades (or did I imagine that?).