It varies. Sometimes they will visit sometimes they won't. I've been on a retirement extension of stay for 8 years, in the past 2 years I've had 3 visits and prior to that none.
Because you're only on a 90 day visa I don't think you need to worry about 90 day reports. However you have only been stamped into the country for 90 days so you need to visit your local immigration office before that expires to get a 60 day visiting family extension of stay based on having a Thai wife. Take your wife along with you