Just chiming in here, but my guess would be that certain things on the pages the shortcodes were put on would no longer work if you disabled the plugin. Let’s say you had a shortcode called [form] that put a form in a page. If you removed the Widget Shortcode plugin it is likely that the page the shortcode was on would load, but instead of the form you expected to be there you’d just see [form] in the middle of the page.
An easy way to test this that should work would be to use the Health-Check plugin made by the fine folks in The www.ads-software.com community. It has something called Troubleshooting Mode. Troubleshooting mode allows you to have a clean WordPress session, where all plugins are disabled, and a default theme is used, but only for your user until you disable it or log out. Site visitors and anyone else logged into the site see the normal site. I’d enable your theme, the Widget Shortcode plugin, and whatever other plugins are necessary for the site to display normally. Then deactivate the Widget Shortcode plugin and browse the website in the same browser to see what pages the short code may display like I said before. Once you are through looking around you can disable Troubleshooting Mode to see the site normally again. Again, this only affects your logged in user. No one else would see anything other than your site as it normally displays.
As Pete said, he passed the suggestion to add more detail to the plugin warning. That team will consider adding it to a future release. However, and this is my opinion, it would extremely difficult to anticipate what every single site would do if you deactivated a plugin. Plugin authors, them authors, and even users like yourself, they find new ways to do things and make WordPress work the way they want it every day. Even if we were to give a vague idea of what could happen there would be a chance that it affected something else and that user might be terribly upset because we didn’t anticipate that result. The people that install the plugins on their sites, they are ones in the best position to know what plugins are installed on the site, how those plugins work, and what they interact with.
I hope the Health-Check plugin helps.
Mia