, 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.