Is it recommended to encrypt files stored via cloud. For example, although certain cloud repositories encrypt data in transit - should I still use a secondary encryption tool for cloud storage?
Depends on what your needs are.
Do you trust the cloud storage provider to have implemented encryption in transit and in rest correctly?
Do you trust that the cloud storage provider won't access the files themselves, or allow others to access them (on purpose or through hacking) - if that is possible with the security model chosen by the cloud storage provider?
If not, you could consider encrypting the files themselves before you place them in the cloud. Is it worth it for a copy of last year's birthday greetings card for Aunt Betty? Is it worth it for a copy of the book keepings of your company?
It really depends on what you need to store (how sensitive it is) and how much hassle you can live with to mitigate the risk of having the cloud storage provider's security (or lack of) broken.
If you do choose to encrypt, it will give you more hassle as you'll need to manually encrypt and decrypt files in order to access them - or rig some kind of automated system for doing the same, without sacrificing security.