Of course heatsink efficiency will deteriorate.
Dust would be the main source of deterioration. The obvious way to slow this process is to install fan filters at all your INTAKE fans. And good news! You can even REVERSE this deterioration by blowing away the dust! Awesome!
Also, thermal pastes can deteriorate and dry up. Not much can be done about it. You can change your paste to something that won't dry up too fast, or just reapply every few years.
Fans can also deteriorate. You can oil that, or change the fan entirely.
Other than that, there's nothing else I can think of that you can do. Other sources of deterioration would include heatpipe deterioration (if you use heatpipes).
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