Is it a good practice to perform backup and restore the farm\web application from backup and restore option of Central admin? Are there any known issues or limitations for that?
Powershell is the suggested way to backup either farm or specific site collections.
It will give you more control over the activity and you can monitor the progress easily.
As a starter you may try from Central Admin, then you can try, But from CA its not good practice .
If you want to know How to do and various options available refer
There are no such limitations but it will be always advisable to use the powershell/STSADM command prompt for these backup/restore activities. mainly because it can take long time and when an error occurs it may hang and you wont be able to get the exact status.
if its in powershell you can very well see the final status very clearly.Also, SharePoint provides excellent API support such as content deployment jobs and so on.