In 2050 SR DID have nanotech; it simply wasn't the level of nanite action you saw after the Arcology Shutdown. Nanites in that time were less 'micro machines' than they were 'magnetically-guided carriers', necessary for the implantation of quite a few different sorts of tech, but primarily nerve-interacting stuff - datajacks, wired reflexes, vehicle control rigs, etc.
I've been chewing on the 'why implant a commlink / cyberdeck / rigger control console if the only way to repair its Matrix damage is by taking it apart?' issue for a little while, and I think I'm split. I believe I'd go with a house rule that blends the two viewpoints: 'surgery' of a sort is necessary, but it isn't too much more than slicing open your head down to the skull, spinning out a couple of screws, and pulling the commlink/cyberdeck out of the slot. There's gonna be blood, and stitches (or at least surgical glue) is going to be necessary, and you're going to take physical damage, even with all that it won't be more than one or two boxes of your Physical track worth.
In regards to dongles, my rule is 'yes, but' - with the 'but' being that the commlink has a port of sorts available, but you're going to have to modify the dongle to fit flush into the commlink, and once it's in your head, it ain't getting changed without surgery (i.e. the above cut-and-unscrew bit). But the essence of the port is going to be there, you just aren't going to be able to switch it out with anything resembling swiftness and ease.