This might be a very silly question, but I wanted to make sure that I am not doing anything wrong.
I am using SLDS to design all my components and has been using js to add necessary classes to perform required action. For example, I had to add slds-is-open class to open a menu item etc.
Is that the right behaviour or the elements should automatically include required class, similar to bootstrap.
Your understanding is correct. LDS is a CSS library and we need to write JavaScript on top of it to add desired behavior. Bootstrap comes with JavaScript handlers and code as well(at places) but Lightning is just a CSS library.
This question in FAQ has the answer to what you are looking for: Is any JavaScript included as part of the framework?
If you haven't checked lately, review the lightning: components listed in the Component Reference and use those where possible. They have the SLDS class handling JavaScript built in and so save you a lot of work.
This Base Components Roadmap suggests that most commonly used components will be available by the end of 2017 (subject to the usual Forward-Looking Statements caveat).
