Ever since I started commercial flying there have been worries about loss of some skills due to automation. I think it's just a fact of life now and the people who write the SOPs are well aware of it.
In the last ten years I have gone from a jet which was still airworthy with no working automation, regularly flying fully manual limiting approaches, to a FBW beast in which we're not even allowed to disconnect the autothrottle...
If I was asked which aeroplane/crew combination was safer for the general public to travel in, I would unerringly point to the more modern airliner and the fact that although it is highly automated, it is incredibly reliable in that respect. I'm not as good as I used to be at "shooting a quick visual" but then I don't think that's a big a part of the job as it used to be.
We have GPS, TCAS, EGPWS, Envelope Protection, etc. which have done far more for flight safety (IMHO) than having "Top Gun" level manual flying skills. OK, so a combination of all would be great but my airline can't afford to give me 10hrs a month in an F-16.
There are more and more flight regimes where manual flight is not encouraged, i.e. most sub-CAT I conditions, RVSM, V-NAV approaches, to name a few. However there is still a need, i.e. circling, ILS PRM breakouts, windshear, etc. for some nifty handling when the chips are down. Not to mention little things like crosswinds, rain and snow.
My personal opinion is that we are relying on a diminishing pool of experience. "Handling events" occur quite regularly in my airline and the management response seems to be to reduce the amount of manual flying allowed in order to limit the risk exposure. Of course, in the long term this will cause more problems but I would never accuse airline managers of thinking long term!
Does the glass cockpit layout encourage much of an instrument scan? I wouldn't say so but we must be careful not to lose the plot here. The 'classic' instrument layout and scan was forced on aviation by lack of technology at the time. Now we can present most of the useful information in one place in any format we like. Do you really 'scan' a HUD? I would guess not as the data is just 'there' for you to assimilate. The better designed the human interface to the aeroplane, the less you need to learn a method of gathering the required information or spend conscious brain power interpreting it.
As an aside, I have to say I've never seen much point in manual flight using a FD. You either follow it, which doesn't need much skill (or practice), or not, in which case why have it on at all?