Having setup Drupal with plans for multi-site use by registered members I can tell you that our preference has been to not use any of the shopping cart modules for Drupal, but to go for software that specializes in being a shopping cart. After looking around we chose ZenCart - YMMV. Similarly, the forum interfaces for Drupal are about as bad as this one here. So we’ve chosen to use SimpleMachines.
This sort of ala carte selection is a pain for many reasons. The code structures are different between frameworks. Integration of user IDs is difficult (we haven’t done this successfully) and solutions like OpenID are half-baked and not fully implemented with all packages. Exchanges of any other information needs to be done with unique code. Package maintenance is all done individually. Common theming across all apps is a problem because stock themes aren’t compatible so you need to do a lot of CSS customizations to get your colors, buttons, and other visual features in sync.
Having said that, it’s a matter of quality versus simplicity. If you want site maintenance to be easy for you, go with an all Drupal solution - and contribute to the code base when possible. If you want the site to be of higher quality for your users, then you have to look at each module on its own merits. Frankly Drupal is a great CMS but each module is subject to the whims of any FOSS package and quality and feature levels vary greatly from one module to another. Everything is in one convenient and consistent package but each module is subject to the same sort of bugs and lack of functionality as any other package on the market. So an ecommerce module in Drupal is not “Drupal” and the default forum mechanisms in the Drupal core are limited and they’re not going to get much better unless you yourself make them better.
Personally I prefer to use software that was written to accomplish specific tasks because the authors are more intent on functionality than making the software work within the context of some larger framework. That’s not an absolute rule, just an observation and perception.
Another option we’re considering as a plan B is to go with an All-Drupal solution just to get smaller sites off the ground and then swap out major modules like shopping cart or forum as it becomes necessary.
Your milage may vary, no guarantees implied, batteries not included, void where prohibited, ask your doctor…