If you’re using GPL libraries in your application and distribute that application, you also need to distribute the source.
Don’t need to be in the same package, but you should make it accessible and let the users know they can do this.
As your main question:
Now, here’s my question… what happens if some of the plugins (be it plugins either created by the company or by users) use GPL dependencies… Would the GPL dependencies only affect to the plugin(s) or would also infect the host and other closed-source plugins?
The „infection” won’t spread, as the host author doesn’t have control on what you’re using. The author only exposes some APIs.