If you need to access those certs programmatically it is best to not use the file at all, but access it via the trust manager. The following code is from a OpenJDK Test case (which makes sure the built cacerts collection is not empty):
TrustManagerFactory trustManagerFactory =
TrustManagerFactory.getInstance("PKIX");
trustManagerFactory.init((KeyStore) null);
TrustManager[] trustManagers =
trustManagerFactory.getTrustManagers();
X509TrustManager trustManager =
(X509TrustManager) trustManagers[0];
X509Certificate[] acceptedIssuers =
trustManager.getAcceptedIssuers();
So you don’t have to deal with file location or keystore password.