Maksym,
I am afraid it is not a bug.In MyEclipse, Add/Remove Deployments does not automatically deploy or undeploy projects from the server deployment directory unless the server is started. If the server is stopped there is no imperative to publish the changes immediately.If you want to “remove/add” a project and publish the changes to the server irrespective of the server state (started/stopped), then you can force it by right clicking on the server in the Servers view and select ‘Publish’.
Hope this helps. Let us know if you have any questions.
–Swapna
MyEclipse Support