A step-thru Nexus 7 speed is a good choice for daily commuting over small-medium distance.
Make sure you have the most puncture-proof tyres you can find. If the stock tyres prove OK, wait till they are worn out before replacing with Schwalbe Marathon PLUS.
Ideally, bikes should come with rack, fenders, lights all nicely integrated so you can forget about them.

Most everyday commuters use a single pannier bag and balance doesn't seem to be an issue. 2 bags can be a handful to carry but your have shoulder straps.

Fenders are a good idea and essential if riding in everyday clothing on wet roads. SKS chromoplastic are the ones to get, they are better and stronger than anything else and the front has a safety release system which has saved my from embarrassment or worse. All fenders need careful mounting, the stays need to be trimmed and rounded for safety. I prefer a ziptie to the metal hardware at the lower rear fitting. A good Local Bike shop (LBS) should be expert in fitting fenders. Shorty fenders are useless, get full length.

Your rear rack has a bracket for a light, this is the best location for mounting a rear light.
If you wear flouncy skirts then you really NEED a skirt guard. They weight nothing and look colourful so what's not to like.