Hi Kirsty,
David here from ATI Holidays, a self-drive specialist, based in Windhoek.
There a number of lodges that are a little more understanding of the needs of kids than others, I incidentally have 2 kids aged 9 & 5, so I know all about the challenges of keeping them happy!
Up in the Central Etosha area I recommend Andersons, a camp set up with the intention of providing a supervised, child friendly environment. Similarly on the eastern flank Mushara Bush Lodge offers a good base from which to explore the park with kids.
At the coast there are a number of great guest houses, our family favorite would be one of Cornerstone's sea front apartments - Atlantik Sicht is very cool! Tommy's Living Desert Tour is a must with children, as is Jeanne who takes Kayaks into the Walvis Bay Lagoon every morning.
Down in the desert I would look at Desert Homestead; it's easy, relaxed and close enough to park gates to avoid a long early morning drive into the park.
There are of course more quality lodges that understand kids - and there are those that don't.... I strongly recommend that you utilize a local specialist agent that can advise, provide support (Evac cover?) and back-up (maybe a local mobile phone) and invariably get you better rates, and certainly improved car hire prices, when booked as part of a package. There are a number of reputable organizations in Windhoek. Check though that they are TASA and NTB registered and be careful with the car hire contract. Insist on tyres, lights, glass and hub-caps, and zero excess insurance.
One other tip - bring a portable DVD player to keep the children happy!
Good luck and I hope you enjoy a wonderful holiday in Namibia,
David