Bringing hiking shoes with dirt/soil to the US?

Cleaning them thoroughly should be good enough.

Here is what happened when we tried to get in with dirty boots in March 2016.

At Charlotte International Airport, we were spotted and stopped by agricultural inspectors while waiting to collect our luggage. They took us into a separate room and provided us with shoe cleaning stuff. We were made to clean our shoes thoroughly and only let out after the inspectors were satisfied. They were friendly, polite, and entirely reasonable, but we did nearly miss our connecting flight.

Last time I brought hiking boots into the US, the customs form asked two separate questions:

I am bringing (...) (d) soil or have been on a farm/ranch/pasture

I have (We have) been in close proximity of livestock (such as touching or handling)

Since we had been hiking in England, crossing common land grazed by cows, we answered "yes" to the first question. See this question for more information. This was a later trip (May 2018) than the shoe cleaning debacle, we had learned our lesson and nothing special happened despite answering yes.

Just declare the shoes as soiled and let customs officials handle the rest.

I live in Australia, we're an island so these things are strictly controlled. If you've cleaned them well they generally let you through, otherwise they will clean them for you. I actually don't mind the cleaning service, it takes them about 2-3mins compared to my 10min effort.

Yes. It's a problem. Yes, you need to declare it. No, it's not a 'big deal' but you're going to have to stop at the USDA booth and they'll take your shoes and disinfect them with some nasty spray. Having them clean as possible will make it easy. But if they're caked in dirt they're going to make you wait while they do it. Source: Been there, done that. Came back from England during Mad Cow with a backpack. And other trips.

Something to understand here:

Yes, our agricultural inspection people tend to care about mud on shoes--they care about anything that can carry pests or disease that we don't have here (Which is why the lists can seem pretty nonsensical at times--they don't care about the items, they care about hitchhikers.) However, they aren't interested in playing gotcha unless you fail to declare something. If you have any question about whether they care about something you declare it and see what they say--there is no penalty (other than loss of the item--note that in this case the forbidden item would be the dirt, not the shoes) for bringing forbidden materials. The only time they'll actually penalize you (I've seen it happen) is if you don't declare the material.