I wouldn't remove the liner. For one, as you mentioned, it hides wiring etc. It also keeps debris (rocks, mud, water, dirt, children, etc.) from getting thrown up into the engine bay and making everything dirty or causing damage (rocks and children are pretty substantial).
All jokes aside though, I would keep them in place as road debris and liquids you may drive through/wet conditions could lead to some after effects that you don't want.
Also, if for some reason a wire harness clip from the fender/engine bay were to break or get damaged and you ended up rubbing tire/rim against the wire loom, not only would you likely cause some major electrical damage due to shorting things etc. if you cut the wires or pulled wiring out, you would have a car that couldn't even limp home at that point. I can't see any reason for the car being so low that you rub the liner... and if your front wheels are properly sized/front tires properly sized you should be able to go reasonably low without rubbing anything.
If you need it wider in the front than fits, or lower than doable, you can get mudflap material from a truck stop, or similar material elsewhere, and make your own covers for the front wheel well, to protect the bay and the wiring. If you go the mudflap route, or decide to disregard my earlier warning/recommendation to put them back on, I would definitely recommend adding additional wire loom/protection to ALL of the harness that is now exposed, and additional clips/fasteners to keep everything in place.