How can I reset tmux's automatic session name numbering?

try:

tmux kill-server && tmux

No, this is not currently possible.

The only thing you can do about this without restarting the server is to override the name manually when creating a new session by issuing tmux new -s 5, for example:

$ tmux new -d -P
10:
$ tmux ls
10: 1 windows (created Wed Jan  7 15:50:29 2015) [107x89]
$ tmux new -s 5 -d -P
5:
$ tmux ls
10: 1 windows (created Wed Jan  7 15:50:29 2015) [107x89]
5: 1 windows (created Wed Jan  7 15:50:40 2015) [107x89]
$ tmux new -s 5 -d -P
duplicate session: 5

---

The automatic session number is governed by the global variable u_int next_session_id in session.c which cannot be accessed from the command line, as grepping the source code reveals.

tmux new-session calls session_create() in session.c (line 88) and next_session_id is incremented whenever you create a new session. The argument of -s flag to new-session (short new) sets name, otherwise next_session_id is used.

     if (name != NULL) {
              s->name = xstrdup(name);
              s->id = next_session_id++;
     } else {
             s->name = NULL;
             do {
                     s->id = next_session_id++;
                     free(s->name);
                     xasprintf(&s->name, "%u", s->id);
             } while (RB_FIND(sessions, &sessions, s) != NULL);
     }