The power was my main concern, but then I realized that maybe even attaching devices that are self-powered, I could still get in trouble with enumeration of the USB ports if I have too many devices.
You are not close to the USB limits in terms of device count or power (assuming you have compliant devices and they're connected to appropriate ports).
Both my previous desktop and my current laptop, at times, just lose devices when too many are plugged in. I think the most I can connect before degrading performance is 8.
You should be able to use all of the ports on any hub simultaneously if you are not exceeding its power limits.
A non-powered hub has to supply power to all of its ports with what is left over after powering itself from the power it receives via its single USB connection to the computer. So all of the connected devices need to be low-power-demand devices.
Self-powered devices get a low-current USB connection, so they should not put high power demands on a port. They're good devices to connect to a non-powered hub. You might want to verify that their power adapters are not defective (e.g., does the device work, or at least indicate that it has power, when it is not connected to the USB port).
Not all devices are well-behaved, so if you are having problems with low-power devices on a non-powered hub, try replacing it with a powered hub.
A powered hub should be supplied with enough power from its own power adapter to provide full USB power to all of its ports simultaneously. As long as none of the attached devices try to draw more power than the USB limit (which would make it a non-conforming device or defective), power should not be a problem. However, check the rating on the hub's power adapter to verify that it is sufficient to power all of the ports (we recently had a question about a powered hub and the hub's power supply was inadequate).
I'm not familiar with the data levels of all of your devices. All of the data for all of the devices on a hub has to be funneled through the single connection between the hub and the computer. If you exceed the bandwidth of the hub's computer connection, you could see some performance degradation, but that would not manifest as losing devices.
The symptoms you describe of losing devices sounds like either a power issue or defective hub or port if it isn't due to a defective or malfunctioning device (if it's always the same device that gets lost, especially if that is regardless of where it is connected, suspect the device).
If I connect another two powered USB hubs, would I be able to plug all the devices permanently, and not overload the system, or is there a USB limit that would require connecting-disconnecting peripherals based on usage?
You can connect as many hubs as you want to the computer's ports, even connect hubs to those hubs. Each USB bus allows a maximum of 127 devices, and each hub counts as a device against that limit. You can connect a chain up to five tiers of hubs. You will want to use powered hubs if you daisy chain them.
USB hubs in general have a reputation for being crappy hardware with high failure rates. If you are using USB hubs and have problems with devices connected to a hub that you shouldn't have because you aren't violating any USB limits, the hub is one of the first things I would check.
To summarize things to check:
- Verify that the only devices connected to a non-powered hub are self-powered or low-power devices. Consider replacing the non-powered hub with a powered one.
- Verify that the power adapters are functioning on self-powered devices.
- Powered hubs sometimes have a switch to set whether they will be operated as powered or non-powered. Verify that the switch is set to powered if there is one.
- Check the rating on the hub's power adapter to verify that it is sufficient to power all of its ports.
- If the same device is lost repeatedly, try connecting it to another port, especially on another group of ports. For example, if it loses its connection on a hub, try connecting it directly to one of the computer's ports. If the device acts up regardless of where it's connected, suspect the device. You could try it on another computer to see if it fails there, also.
- If the problems are with multiple devices on the same hub, try connecting the hub to another port on the laptop, especially one in another location on the laptop if there is one. If it's problematic there, also, try another USB hub.
Those are all simple things to check to rule out the common causes. If none of those solves the problem, update your question with the details and we can try a bigger hammer.