Can we load master data through RDA DTP?

No. 

RDA is basically used from Transaction data and not all the Data sources are enabled for RDA.

To find whether a data source supports RDA, you can check in the table ROOSOURCE (Field REALTIME = 'X'),

what are the difference B/W loading data using SAP API and Web services. we generally use SAP API for SAP source system and for other Web services. I am i right?

Yes.

Webservices are used to Push the data to BI from the Webservice based messaging systems (Middleware like XI, TIBCO Etc).
Where as Service API (SAPI) is used to Pull the data from SAP Source systems to BI.