I understand your concern for the babies to potentially drown, however, I like to err on the side of caution in the other direction. I'd rather that I risk one baby possibly drowning than risk all of them possibly becoming dehydrated.
For all of my baby snakes (regardless of species) I use small Gerber baby food bowls. You can find them in the baby food section of whatever store you prefer to shop in. They are small enough that the babies can easily access them to get a drink but not so large that there really is a risk of drowning. Plus, if and when one of them is knocked over the amount of water in the bowl doesn't end up soaking the entire tub.
Other people use small deli cups that they purchase in bulk. These can be placed inside of a PVC end cap to prevent tip-overs and spills. I used to go with this method but since I've downsized my collection, I really don't need to purchase as many things in bulk anymore. The advantage of deli cups is that they are generally cheap enough to simply be thrown away (or recycled - the better option) which can cut down on the time spent in the snake room if this is an issue for you.
With the Gerber bowls I usually do end up washing them by hand. Every neonate in my collection gets them in their individual tubs and when I have fresh hatchlings (I don't breed my boas - yet!) I place two to three of the bowls in the "community-shed-out" tub. This helps eliminate competition for water and allows me to spread them out in the tub so that all of the hatchlings can easily find the water they need since they aren't as likely as adults to venture far looking for water.
-----
.
.
.
.
Stay United!

I'm still not sure if it's weird that my best friend is a two year old boa named Ronin. He's quiet, non-judgemental and listens... what more could you want?