Sure, you can use the same realism settings as normal, you're not forced to use manual targetting or no weapon officer help or no cameras or anything. Newbies will be able to play just fine really. To be honest, the only "vanilla" SH3 I played was the Navigation tutorial. After that I liked the game so much I looked for add ons and have been using GW (and lately NYGM) since "the beginning" for me.
A few things you will find more difficult and cannot easily change are:
Damage model is changed. Ships sink by flooding rather than just damage. Meaning you need to hit multiple times in various places and wait longer for a ship to sink now.
Along with the above, deck gun is slower, does more damage per hit, but is less effective due to the above changes to how a ship sinks. Previously a ship had X numbers of hit points and if you exceeded that, say by shooting the bridge with your deck gun, you'd sink the ship. No longer.
All contacts are grey. No more red = bad guy, green = neutral. You'll need to risk and approach to get close enough to ID a target now. Sometimes you'll end up creeping up and getting into firing position of a friendly tugboat, othertimes not.
That said, it's a superb mod and definately worth running. It's beautiful, more lively and really adds enough to the game that even with it's more difficult aspects it's rewarding and enjoyable.
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