Good questions. :)
Plants most definitely take up nutrients from the soil. A heavy feeder like corn is hard on the soil - one of the reasons they rotate with soy on factory farms is that corn simply requires a LOT of nitrogen and won't grow well after repeatedly being sowed on the same plot of ground without replacing the lost nitrogen. Other plants aren't quite so hard on the soil.
But this is viewing soil simply as a transfer mechanism for chemicals like NPK and not the right way to look at things in my opinion. Rather, the soil is a living, breathing community of organisms (might sound a bit silly, but this is the truth) which break down compost and manure and aerate the soil and make it quite conducive for growing plants. So adding some compost to the soil is a good thing because it helps feed the soil.
If you fill your beds to the brim they will settle a bit over time but there will come a point where they are definitely full.
You have options. A couple of which are:
Add some compost/manure/worm "tea" to the beds. This is a kind of "liquid fertilizer" that adds nutrients and organisms back into the soil. I've generally just taken, say, worm tea and spread it on the soil prior to planting or later on as a side dressing to the plants. Seems to work quite well.
If you are so inclined, you could shovel off some of the topmost soil into a wheelbarrow and use it for a new bed, or some containers or add a little bit to a compost pile or even spread it on the lawn. Then you could mix in some new composted manure or compost to the soil. That's a bit more labor-intensive but not that bad.
Honestly, I've never got to the point where I was so overloaded with soil because I will tend to just add another bed or a couple of containers or a lettuce table. I do tend to pull a bit of the soil off my beds when creating new seedlings or containers and then will head over to the compost bin and grab a few loads of compost to mix in to the beds. This helps to keep the beds healthy and filled with microbes and nutrients (and worms!). So it's a process and requires some inputs from somewhere, whether that is tilling in a green manure or amending it with manure or compost. You'd end up with the "dust bowl" situation if you never amended the soil and were only ever removing nutrients from it. Legumes will "fix" the soil with nitrogen but there's more to growing than just nitrogen.
A bit long, but I hope that was useful.