Both our Gurlies who were done earlier this year were done "through the side" too. The technique differs from vet to vet, and some use dissolving stitches, others use old fashioned style sutures.
Neither of the gurlies had to wear a collar. They did lick the wound site from time to time, but as Paula said, it didn't do them any harm, and as I recall, both resumed tearing round the house again in fairly short order.
I would say try her without the collar and see how she goes. An unhappy cat will take much longer to settle down.
Many years ago, the only other female cat we had neutered was a slightly different scenario.
She went into post-operative shock. She ended up having to spend 3 days with the vet, and then nursing with us for almost a week before she recovered.
You do right to keep an eye on Bonnie, but I suspect she may just be taking a bit longer to shake off the effects of the anaesthetic and post-op recovery.
If you're still concerned later this morning, I'd give the vet a quick call to outline her progress and ask whether you need to take any further steps. I'm sure she'll be fine.
Please let us know how you get on.