Yes, putting pebbles in it is a good idea. Definitely don't leave an open dish with water near them, as they can drown or get wet. I use one of those small, jar type of waterers, meant specifically for chicks, so they are safe:Thank you!
One more thing - I currently have her food dish and a shallow water dish (hard to describe - it's a piece of our old fine China, lol) close to her which has been working well. During those first couple days you mention after hatch, when she stays put with them, should I use a little larger dish for the water, with maybe a layer of washed pebbles for their safety?
(I use vertical nipple waterers in the coop for after that, which mom already uses. )
Keep in mind that the chicks may not be able to operate the nipples for a while. Vertical nipples are easier for them than horizontal nipples, but it's still an unnatural way to drink and they'll need to learn. You don't want them getting dehydrated while they figure it out. So you can provide both a nipple waterer and a non-nipple waterer at first, to make sure they're getting enough water, and hopefully the hen will teach them how to use the nipples. Vertical nipples are more of a challenge than horizontal though because they need to be at the right height to be used, and the chicks will grow very fast. So you'll need to keep changing the height. Also, the hen may not be able to reach the nipples at chick height to teach the chicks how to use them. So you'll need to be more involved.