I'm using GNU NNTP to connect to leafnode, which is an NNTP server, on localhost.  The GNU API utilizes javax.mail.Message, which comes with the following caveat:
From the Message API:
..the message number for a particular Message can change during a session if other messages in the Folder are deleted and expunged.
So, currently, I'm using javax.mail.search to search for a known message.  Unfortunately, for each search the entire folder has be searched.  I could keep the folder open and in that way speed the search a bit, but it just seems klunky.
What's an alternate approach to using javax.mail.search?  This:
    SearchTerm st = new MessageIDTerm(id);
    List<Message> messages = Arrays.asList(folder.search(st));
works fine when the javax.mail.Folder only has a few Message's.  However, for very large Folder's there must be a better approach.  Instead of the Message-ID header field, Xref might be preferable, but still has the same fundamental problem of searching strings.
Here's the database, which just needs to hold enough information to find/get/search the Folder's for a specified message:
mysql> 
mysql> use usenet;show tables;
Database changed
+------------------+
| Tables_in_usenet |
+------------------+
| articles         |
| newsgroups       |
+------------------+
2 rows in set (0.00 sec)
mysql> 
mysql> describe articles;
+--------------+--------------+------+-----+---------+----------------+
| Field        | Type         | Null | Key | Default | Extra          |
+--------------+--------------+------+-----+---------+----------------+
| ID           | bigint(20)   | NO   | PRI | NULL    | auto_increment |
| MESSAGEID    | varchar(255) | YES  |     | NULL    |                |
| NEWSGROUP_ID | bigint(20)   | YES  | MUL | NULL    |                |
+--------------+--------------+------+-----+---------+----------------+
3 rows in set (0.00 sec)
mysql> 
mysql> describe newsgroups;
+-----------+--------------+------+-----+---------+----------------+
| Field     | Type         | Null | Key | Default | Extra          |
+-----------+--------------+------+-----+---------+----------------+
| ID        | bigint(20)   | NO   | PRI | NULL    | auto_increment |
| NEWSGROUP | varchar(255) | YES  |     | NULL    |                |
+-----------+--------------+------+-----+---------+----------------+
2 rows in set (0.00 sec)
mysql> 
While the schema is very simple at the moment, I plan to add complexity to it.
messages are queried for with getMessage():
package net.bounceme.dur.usenet.model;
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.mail.*;
import javax.mail.search.MessageIDTerm;
import javax.mail.search.SearchTerm;
import net.bounceme.dur.usenet.controller.Page;
public enum Usenet {
    INSTANCE;
    private final Logger LOG = Logger.getLogger(Usenet.class.getName());
    private Properties props = new Properties();
    private Folder root = null;
    private Store store = null;
    private List<Folder> folders = new ArrayList<>();
    private Folder folder = null;
    Usenet() {
        LOG.fine("controller..");
        props = PropertiesReader.getProps();
        try {
            connect();
        } catch (Exception ex) {
            Logger.getLogger(Usenet.class.getName()).log(Level.SEVERE, "FAILED TO LOAD MESSAGES", ex);
        }
    }
    public void connect() throws Exception {
        LOG.fine("Usenet.connect..");
        Session session = Session.getDefaultInstance(props);
        session.setDebug(true);
        store = session.getStore(new URLName(props.getProperty("nntp.host")));
        store.connect();
        root = store.getDefaultFolder();
        setFolders(Arrays.asList(root.listSubscribed()));
    }
    public List<Message> getMessages(Page page) throws Exception {
        Newsgroup newsgroup = new Newsgroup(page);
        LOG.fine("fetching.." + newsgroup);
        folder = root.getFolder(newsgroup.getNewsgroup());
        folder.open(Folder.READ_ONLY);
        List<Message> messages = Arrays.asList(folder.getMessages());
        LOG.fine("..fetched " + folder);
        return Collections.unmodifiableList(messages);
    }
    public List<Folder> getFolders() {
        LOG.fine("folders " + folders);
        return Collections.unmodifiableList(folders);
    }
    private void setFolders(List<Folder> folders) {
        this.folders = folders;
    }
    public Message getMessage(Newsgroup newsgroup, Article article) throws MessagingException {
        LOG.fine("\n\ntrying.." + newsgroup + article);
        String id = article.getMessageId();
        Message message = null;
        folder = root.getFolder(newsgroup.getNewsgroup());
        folder.open(Folder.READ_ONLY);
        SearchTerm st = new MessageIDTerm(id);
        List<Message> messages = Arrays.asList(folder.search(st));
        LOG.severe(messages.toString());
        if (!messages.isEmpty()) {
            message = messages.get(0);
        }
        LOG.info(message.getSubject());
        return message;
    }
}
The problem, which I'm only now realizing, is that:
...the message number for a particular Message can change during a session if other messages in the Folder are deleted and expunged.
Regardless of which particular header is used, it's something like:
Message-ID: <[email protected]>
or
Xref: dur.bounceme.net gwene.com.economist:541
So that there's always a String which needs parsing and searching, which is quite awkward.
I do notice that MimeMessage has a very convenient getMessageID method.  Unfortunately, GNU uses javax.mail.Message and not MimeMessage.  Granted, it's possible to instantiate a folder and MimeMessage, but I don't see any savings there in that from one run to another there's no guarantee that getMessageID will return the correct message.
The awkward solution I see is to maybe create a persistent folder of MimeMessage's, but that seems like overkill.
Hence, using a header, either Xref or Message-ID and then parsing and searching strings...
Is there a better way?
                        
javax.mailis a lowest-common-denominator API, and it's behavior depends entirely on what is the backend. So, without knowing what you are talking to, it's not really possible to give a good answer to your question. Chances are, however, that you'll need to talk directly to whatever you're talking to and learn more about its behavior.This might be a comment rather than an answer, but I'm thinking that the information that this API is just a thin layer might be enough information to justify.