Not only the power pins, but the GPIO pins have practically no protection either.
Regarding networking, there are more options besides ethernet, you could use the serial port on the thing and PPP over it, at least one UART is on the header if I'm not mistaken.
To connect them together, you'd need a way to have them all feed back to one Pi just doing the PPP to Ethernet bridging and you can use it's existing ethernet connection to plug in to your network. It would take some sort of expander or multiplier to get all those serial connections connected back to that one Pi, so an extra chip is still needed, but only one and not one for every Pi. The nice thing about Linux is that as long as something does stuff like TCP/IP, any application running on top of it won't know or care about what transport is used on the lower levels. There is support for at least serial, parallel, usb, ethernet (of course), firewire, pcie, IRDA, ISDN and a while back someone was working on TCP/IP over I2C (but I'm not sure if that was ever completed).
With the networking thing on the hardware side, there is a software side too: proper hardware has MAC addresses for network interfaces on Ethernet, and other busses have arbitrary configurable or serial number based addresses in many cases. If you were to want to configure your cluster in a somewhat automated manner, you could just have the IP addresses preconfigured based on those addresses in a DHCP server. The compute module would request an address, the DHCP server would recognise it's MAC address or port ID and assign it the correct address.
Regarding the Software, the Raspberry Pi guys have 'Raspbian' which is a modified version of Debian, specifically for the Pi. Since Debian is completely free/libre/open/wank-word-of-the-day and the process of adding Raspbian modifications on top of it is documented, the software should always be maintained and maintainable. There is no secret sauce or a commercial entity required to keep it going on the Linux-based side. On the bootloader and GPU side of things, it's a bit tricky, since Broadcom still thinks that has to be 'secret sauce' for some reason (as if nobody else has a CPU that can boot... or a GPU that does graphics). There is the bootloader binary blob file that reads config.txt, and that's the part you can't really maintain if you're not a broadcom-zombie, so that's something that may not always be kept up-to-date. On the other hand, does it really need to be 'maintained', since it's just there for one thing: initialise the GPU, and start it, then let it start the CPU (yes, that's how the thing does it) and setup the DRAM, and kick the kernel into action. So as long as the hardware doesn't change and the kernel is fine with whatever the bootloader parks in memory, it should work indefinitely.
For other boards, this may not work out so well. There is this Banana Pi, and the Orange Pi, and there are probably a ton of other Pies (enough to fill a pastry cookbook?), and we have the 'chip' and then there are the minnow boards, beagle bones, and LeMaker is doing stuff, and everyone is coming to join the club. Specs-wise, that's nice, but when it comes to software, unless you have one of those Linux distributions (like Debian or Fedora) to build on and a platform specific community (like with Raspbian) to maintain tweaks for the board-specific things, it's impossible to maintain or develop in a workable and long-term way, because the resources are simply not there. Since software and the internet (and everything connected to it) is always changing, at some point, you'll always have to update, upgrade or modify the devices and/or software in order to keep using it or keep it connected to others. Try finding a serial modem, or an IrDA adapter, heck, try finding an analog phone line! It's annoying, but as long as stuff is connected or has to work together, everything has to keep up. (up to a certain level, of course)
So when picking a board or software distribution, the community or upstream projects feeding the software that runs it are about just as important as the hardware specs themselves.
Without good software, those tiny boards won't even cut it as a paperweight (too light to hold anything down!).