I've been toting my 17" laptop in my side cases for a bit. Never any issues, although I did upgrade my hard drive recently. Not spending much time at all on the bike these days (needs some work thanks to a bad spill), but I used to bring my 17" laptop to work with me (60 mile round trip) 2-4 times a week.
48K on the bike, laptop was with me, in either of the side cases, for at least 30K of those miles...
Also packed my laptop on a few longer jaunts (500-600 miles).
The only 'padding' is the backpack. My 17" laptop barely fits in the side case inside the backpack, so top/bottom padding wasn't really an option in my situation.
Unless your HDD has been giving you issues already, then I wouldn't be too concerned. Another option (if you are worried) would be to put it in a carry on suitcase and strap that on your back seat, cushioning it between clothing that you may be bringing with you.
Long term wise, SSD's are nice for a lot of reasons, lack of moving parts being one of them. They do degrade eventually, but endurance values these days are pretty robust. In most cases (unless you are a REALLY heavy user), these days the laptop will probably die from other factors (screen failure, etc.) long before the SSD degrades significantly...
I do have some rubber cushions inserted between my antler and the pad the antler rests against, which might help reduce the 'bouncy bouncy'/side to side jolts. That's just good in general, for those that haven't already permanently bolted the antler to the pad.