You are confused on this.
A keystore
is a container of certificates, private keys etc.
There are specifications of what should be the format of this keystore and the predominant is the #PKCS12
JKS is Java's keystore implementation. There is also BKS etc.
These are all keystore types.
So to answer your question:
difference between .keystore files and .jks files
There is none. JKS are keystore files.
There is difference though between keystore types. E.g. JKS
vs #PKCS12