My Apple II has been getting really hot in use, I've cleaned it, so I don't think dust is an issue. Is there something wrong with the hardware that could be affecting it? I've had Apple IIs overheat and break before, so I'm not sure if it was a factory issue or something that affected all Apple II computers.
The Apple ][ could overheat if it had a number of cards installed. Especially if they were close together. So, yes, it affected (almost) all of them.
This would affect the airflow within the case and heat would build up.
Back when I used Apples, I would try to have a blank I/O slot between each populated slot. That would get the air flowing better.
I know certain cards got picky about which slot they were installed in, so your options may be limited.
Also, try not to block the slots at the back of the case with cables. The slots are to enable cables from the cards to pass through the case and connect with peripherals. However, bunging them up with cables can also impede airflow.
You don't say if you have any installed cards, or how many. In my experience an Apple with a minimal number of cards would run forever without overheating.
A very common add-on for the Apple II was called the Kensington System Saver. This is a "Muffin fan" that hooked into the vent slots on the left side of the Apple II/II+/IIe, had a front-side master power switch, and 2-3 outlets on the back to power the computer, monitor, and printer.
This fan noise was a very characteristic sound for Apple II computers in schools, as you'd have a room of 20 Apple II's outfitted with System Savers.
Google image search: "Apple II" "System Saver" -- http://www.google.com/search?tbm=isch&q=%22Apple%20II%22%20%22System%20Saver%22
You can probably still find it on eBay.
For the Apple IIgs, it did not include a fan as a standard feature from Apple but it does include a place to clip one on to the power supply at the front corner, and a 2-pin plug on the motherboard for a fan.
Though the placement of the IIgs internal fan is weird, inside the case directly on the power supply, and I don't know if it actually pushed hot air out of the case or if it just blew the air in a circle inside the case, which would not have been very effective for cooling.
Kensington also made a System Saver IIgs which sat on top of the computer, under the monitor, with power switches across the front, and a fan to suck air up through the top of the IIgs and blow it out under the monitor. There was a rubber gasket around the edges to seal the System Saver IIgs to the top of the computer.
Google image search: "Apple IIgs" "System Saver" -- http://www.google.com/search?tbm=isch&q=%22Apple%20IIgs%22%20%22System%20Saver%22
If you are one of the lucky few to still own an Apple ///, you already know all about its overheating problems which were legendary for its time and which caused the untimely death of the system.
It ran extremely hot due to Steve Jobs' idiot insistence that fan noise sucks and air vents are unattractive. Socketed chips would slowly work themselves out of their chip-holders causing electrical failures. An official solution to this from Apple was to pick the machine up and drop it on the table to reseat the chips.
Reference: Wikipedia - Apple III https://en.wikipedia.org/wiki/Apple_III