Several of the Harrison Forman photos show ARP tunnels under construction. On some (eg this one), it is possible to see a number above the entrance. Here's what I think the different numbers mean.
First there are the Site Numbers. I believe these were the original numbers used, assigned to each construction site where tunnels were dug. Guessing again, I'd say they were given out in the order that sites were decided upon, so earlier sites have lower numbers.
There are some gaps in the list of sites. eg we have 1..11, and 13..16, but no number 12. It seems unlikely that numbers would be skipped at random, so I guess either a missing number is either a site we don't know about yet, or it was a site where some other ARP work (eg trench shelter?) was carried out.
Next are the Tunnel Numbers. These are the numbers shown above a tunnel during its construction. I believe these were just used during construction, as the contractors needed to keep records for each tunnel (number of workmen, number of feet dug, etc). From looking at some of the old tunnel plans, I think these were assigned per site. So you might get a 'tunnel 1' appearing at several sites.
Then came the Portal Numbers. When construction of the full tunnel network was finished, each of the portals (entrances) to the tunnels was given a number. The numbers start with portal #1 in Kennedy Town, then increase as you move clockwise around the island, finishing at #124 in Aberdeen. Again there are gaps in the list, as some networks aren't publicly documented.
Finally we see current records use Network Numbers. eg the tunnel network under Hospital Hill is Network 10. The Network Numbers used are the same as the Site Numbers - so what was called Site 10 is now called Network 10.
Re: ARP tunnels: numbering systems
An example of this system from the newspapers dated 9 SEP 1941 detailing of a blast that had occurred inside No. 11 ARP tunnel at site No. 23, Aberdeen.
It was stated at the ARP enquiry on 16 SEP 1941 that all sites on Hong Kong Island, with the exception of the Aberdeen tunnels, had been completed.