Haha that's a kind of a funny image --- to net the entire garden to keep out squirrels.
Actually I think the deer netting suggestion was for a smaller scale protection of container planting and flower beds?
My observation of squirrels in my garden is that they either dig to unearth treasures -- acorns and other tree nuts -- they buried or to bury them. And they do think windowboxes and gallon size and larger containers are good places to bury them. I have found dug up pots and have also uncovered buried hickory nuts, have had volunteer tree seedlings grow, etc.
Squirrels will dig in garden beds that you have thoroughly turned over and removed those buried nuts if they suddenly remember that they happened to bury treasures there. I remember yelling at them that the nuts aren't there anymore and to look for them along the back fence where I tossed them.
In larger garden beds, squirrels sized holes dug here and there are not all that significant.
It's best to individually protect new seedbeds or young seedlings -- birds, chipmunks, mice are the ones that tend to dig them up and eat the seeds, and rabbits and occasionally groundHOGS eat the little seedlings in my garden (no deer here). Garden fence to keep out the seedling eaters and low tunnel with netting or floating cover seems to help under most circumstances. Mice will get inside tunnels, though.