The difference is mainly that the orapki tool is dealing with certificates rather than the wallet itself. The mkstore is more of a tool for administrating privileged users and their passwords, so that you can set up connections without exposing their passwords in your scripts.
Can both of these tools be used to manage my wallets?
Yes.
From MOS Doc ID 2044185.1 "What is an Oracle Wallet?":
If you configure TDE the database creates the wallet for you when you issue the ALTER SYSTEM command to initialize TDE, the other tools to create and inspect wallets are Oracle Wallet Manager (owm) which is a GUI tool, then we also have command line tools orapki to setup certificates and mkstore more suited to store so called secret store entries like the above mentioned user credentials, often the tools can be used interchangeably, for example if you create a wallet for TDE using the database with SQL you can inspect the contents later using mkstore etc.
What exactly is the orapki tool?
From the latest Oracle documentation:
The orapki utility manages public key infrastructure (PKI) elements, such as wallets and certificate revocation lists, from the command line.
What exactly is the mkstore tool?
From the latest Oracle Documentation:
The mkstore command-line utility manages credentials from an external password store.
What exactly is a wallet?
A wallet is a password-protected container that is used to store authentication and signing credentials, including private keys, certificates, and trusted certificates needed by SSL.
It can be stored directly on the server, wherever suits the DBA. The path must be pointed out in the client's sqlnet.ora file, using the directive WALLET_LOCATION
For an example on how to set up a wallet, see this post
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