I would honestly be surprised and somewhat disappointed if Apple DIDN'T replace all (or at least most) of the USB-A ports with USB-C. Of course like everyone else here I have lots of USB-A peripherals and will likely need to buy a hub (or an adaptor for the hub I already have) to connect them.
Why don't I want USB-A ports then, you ask? Simple. USB-C is the future and I'd rather be slightly inconvenienced now, then IO limited down the road (or even today).
Embarrassingly enough, Apple is already one of the last major computer manufactures to get (the majority of their computers) on the USB-C train, and once they are on board there will be little incentive for manufacturers to produce new USB-A devices.
That means, going forward, the vast majority of new peripherals will be using USB-C. Sure it will be an inconvenience at first (just as USB and FireWire were when Apple replaced the connectors of old with them back in the days of the Bondi Blue iMac and Blue and White PowerMac G3), but two years from now when you no longer have USB-A devices to plug in you'll be glad not to have valuable IO space wasted with USB-A ports that you never use (particularly given how stingy Apple already is with ports).
This concern becomes even more pertinent when you consider that while Thunderbolt 3 and USB-C share a port, Thunderbolt 3 supports daisy chaining while USB-C does not. This means that if Apple set up the IO configuration similar to how it is done today (with two USB-C/Thunderbolt 3 ports and four USB-A ports), you could end up with a nightmarish IO scenario where you have to position USB-C devices at the end of a Thunderbolt 3 chain, and if one of your devices doesn't want to play ball you may just be SOL.
I feel the pain of those who don't want to buy an adaptor, but USB-C is the future, not just on Mac, but industry wide. This is one of those decisions that doesn't just take "courage" (god what a dumb way to explain it to the customer Eddy), but makes sense.