, yes, all applicants have to pay each. It totally depends on the Thai Embassy/consulate if they require you to prove 500K for each or 500K baht equivalent of the primary applicant can cover all family members. Yes, both have to do 90-day reports if staying in Thailand long enough.
She can work only remotely for the company or clients outside Thailand, not for anyone inside Thailand.
The advantage depends on individuals' priority. Someone's pros could be someone else's cons. That is solely your decision.
The check-in date on TM30 does NOT have to be the same as your entry stamp. TM30 is supposed to be submitted within 24 hours after you arrive at that address, not the day you entered Thailand.
Yes, If you have applied for a 1-year extension inside Thailand at the local immigration office, you have to cancel an extension and a work permit.
You can apply for cancellation of a work permit at the labour office and an extension at the issuer immigration office by yourself, but you need a letter from the employer.
In general, you go to the labour office to cancel your work permit by yourself as long as you get a termination letter from your employer then go to the immigration office to cancel an extension using the cancellation receipt of your work permit. But the order and details vary by province. Talk with both offices for details, especially what you need to cancel.
In a rare case, if you have a multiple-entry visa, you only need to cancel your work permit as the visa itself cannot be cancelled. In this case, talk with the immigration office to see if they can "void" that visa.