My experience is different and hibernate does work well the vast majority of the time with notebooks. Since notebooks typically do run off the battery, and since charged batteries do run down, if that ever happens when you are not around to save your data and properly shut down, you need to keep hibernate enabled.
If you keep your notebook plugged in most of the time, most notebooks let you change the power action when you close the lid to sleep instead of hibernate. It might be worth a try to see what happens. Either way, USB devices are supposed to be recognized when the systems they are attached to wake from any power setting.
The problem here is USB 3.0 which sadly, had not had a good track record. USB 3.0 was supposed to fix all the problems USB 2.0 was supposed to fix with USB 1.x.

And I note it is not uncommon for USB devices attached to PCs to no be recognized after they come out of sleep too - particularly, hybrid sleep which is more like hibernation but for PCs which have ATX power supplies connected all the time.
Since your devices do wake properly, just not when in the right ports, it seems apparent the problem here is with USB and sadly, other than making sure you have the most current
Acer drivers for your notebook, and the most current drivers for your USB devices, there is not much you can do. Sorry.