I am shipping my product X version 1. It is installed in folder "%program files%\X V1". It has a sub folder /addins where users will put addins to my product written by the community.
Fast forward to V2. What should be the deployment strategy?
I recommend you for downwards compability not to use the version number in you folder structure. As Jouke van der Maas already said, it would be possibly sensefull to migrate your addins folder to '%user%/My Documents' or '%user%/App Data/Roaming'. Otherwise you will possibly get confused user requests, when the new version comes up.
IMO the only reason to include the version number in the product folder is if the customer wants to have both versions of a product installed at the same time, e.g. Microsoft Studio 8 (2005) and Microsoft Studio 9 (2008). If you look in the Program Files directory you will note that most companies do not include the version number in their folder name.
You should use a separate folder for plugins:
What about a company/appgroup folder (see MS Office)?
Also, you can take a trip into your Program Files folder to see how others do. (Sorry, I can't. I have no such folder for a while.)
In most cases there is no reason to include version number in the folder name. Even if the customer wants to install both versions, then he should give another folder name himself. Only valid reason I can think of is if installing new version in the same folder could potentially cause technical problems and there is no other way around the problem.
And even if you decide to create separate folder for each version, I would use folder structure like this: