Is there any way to overcome the apex limit for total number of SOQL queries issued using custom metadata records?
I guess it really depends on if the data you are querying is data, or metadata?
I think you're possibly referring to using Custom Metadata Types as data rather than metadata?
Whilst it's true that the limits are relaxed for SOQL queries for querying Custom Metadata, using Custom Metadata for data would be both challenging, and a waste of resources. For example, it is not currently possible to insert/update records using DML. Neither is there a UI. This means you'd have to develop your own method of inserting/manipulating data using the Metadata API, not to mention providing a UI.
There are also other features and limitations that I think would prevent you from realistically using Custom Metadata for data. However, if your data is actually metadata, then this is the raison-d'être of Custom Metadata and is ideally suited.
EDIT: as of Winter '16 you can now edit custom metadata type records declaratively.