elle long-term hardware degradation based on usage?
yes. Say you have a Pd patch where you are polling an analog input value and printing it to the console every10ms. I have seen that happen a lot when people develop/debug patches. If you leave that into production, it will write about 1KB per second to the system logs. Until now (i.e.: before the commits linked above), this gets written to disk. Assuming the free space on the device is about 1GB, that space will get filled every 11 days of continuous usage. The logs are rotated, so assuming the disk implements wear levelling, you are erasing and writing it 33 times per year. That's not a lot: flash should withstand at least 10k erase cycles, so it wold last 303 years... With no wear levelling, things would look significantly worse as individual sectors could wear out much faster. I couldn't find the datasheet for all the eMMCs that ever shipped with BBBs. Those I found had wear levelling but didn't report the how many erase cycles they can withstand.
Anyhow, assuming they all have wear levelling (reasonable), now that I put some numbers in, the bottom line is: unless you are logging a lot of data to the console(when running on boot) OR writing a lot of data to disk on purpose (e.g.: recording inputs) OR using the eMMC as swap OR I got my numbers wrong by 3 zeros or more, then the eMMC shouldn't decay because of repeated reads/writes fast enough to cause troubles even if you were to keep it running for 10 years. Anyhow, if for some reason (e.g.: heat?? let's remember you left these things running in the desert!!!!) the eMMC doesn't seem reliable, a new SD card should most definitely be a better option. Note that not all SD cards will have wear leveling so they may wear out much faster, but when they are new they should work without exception.