have been keeping me busy for the last 10 years or so.

the permit or business license or both?

Is the squatter some random person or where they living there at one point and stopped paying rent? 

They are unprofessional, don’t care about people, and apparently completely inept when it comes to business.

One tenant however, did refer to having their rent pro-rated by the number of days that the situation would last.There is a clause in both their leases that they are responsible to carry renters insurance to protect their personal belongings against fire, theft, flood, loss of use etc. 

The subscription service based washes have basically rendered these businesses not viable.

Your journey is two part - accumulate more wealth, and then how you are going to move it onto your kids - both have substantial tax planning opportunities.Given you mentioned your primary motivation is taxes, a HUGE caveat you should keep in mind is that no matter what real estate investment you make, first and foremost it should make good business sense. 

Or are holes after move-out just part of the cost of doing business?

You are looking to see if they are maintaining the home like a normal person or if they are abusing or neglecting the rental.

Would it be under the business tax id number which would be brand new (so no history yet) or would it be through me personally through my own credit report/history?