If you have disassembled the system, and are attempting to clean the inner circuitry of the system (e.g., the circuit board of the 3DS, any components soldered onto it for functionality, card slots and button internals, etc etc.) then yes, it's alright to use isopropyl alcohol to clean your components. Keep in mind though that you should use as high a percentage of alcohol as possible; something within the 91% to 99% total content range would suffice, as you want to limit the water dilution content of the solution as much as humanly possible. Any water that remains on the circuit board when the alcohol evaporates will absolutely have a non-zero chance of possibly causing a short, by way of the electrical pathways bridging through the water from one circuit trace or component to another.
This is why we give the suggestions to let the device air dry for some time afterwards, preferably in a sterile, non-humid and dry location free of debris or dust.
For cleaning the outside as well as the surfaces of the device, and not the interior, it's recommended to not just pour the alcohol onto or into the device; instead, apply it to a soft, non-abrasive microfiber cloth, a non-abrasive cotton swab, or as soft-bristled a toothbrush as you can find, and then clean it with gentle (not forceful) application, wiping and polishing it afterwards with the dry portions of a microfiber cloth, as well as using a protective case of some sort for storage afterwards, in addition to screen protectors for the screens and panels.
EDIT: As an aside, you can order 100% pure IPA (isopropyl alcohol) on websites like Amazon, typically from their commercial cleaning section. You'll have to buy it at possibly bulk prices, and keep in mind the prices are also for commercial usage and purpose, but it is available if you want to be absolutely sure. Keep in mind all advisories provided on the sale page and product as well as proper usage information on the product's labeling, and you should be fine. If this concerns you, continue to buy the 91% to 99% isopropyl bottles from your local drugstore or supermarket.
This is why we give the suggestions to let the device air dry for some time afterwards, preferably in a sterile, non-humid and dry location free of debris or dust.
For cleaning the outside as well as the surfaces of the device, and not the interior, it's recommended to not just pour the alcohol onto or into the device; instead, apply it to a soft, non-abrasive microfiber cloth, a non-abrasive cotton swab, or as soft-bristled a toothbrush as you can find, and then clean it with gentle (not forceful) application, wiping and polishing it afterwards with the dry portions of a microfiber cloth, as well as using a protective case of some sort for storage afterwards, in addition to screen protectors for the screens and panels.
EDIT: As an aside, you can order 100% pure IPA (isopropyl alcohol) on websites like Amazon, typically from their commercial cleaning section. You'll have to buy it at possibly bulk prices, and keep in mind the prices are also for commercial usage and purpose, but it is available if you want to be absolutely sure. Keep in mind all advisories provided on the sale page and product as well as proper usage information on the product's labeling, and you should be fine. If this concerns you, continue to buy the 91% to 99% isopropyl bottles from your local drugstore or supermarket.
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