I do similarly. When the larvae are small, I pour out the water gently until I have just the larvae and a small amount of water left, then add fresh water. Or use the turkey baster. When they are larger (less fragile), I pour them into a regular fish net, then dump them back into a fresh container of water. A brine shrimp net wouldn't be good for this, as it would trap both the larvae and a lot of the dirt. I guess it is stressful to some extent, but only for <1 minute per day. I've never lost any larvae due to this method.
However, if the larvae are being kept in an actual aquarium, it's not really feasible to do 90-100% water changes. In this case, do as much as you can, within reason. And be sure to clean out all debris from the bottom every day.
For larvae, my person feeling is that the best housing are EITHER (a) a well-cycled planted tank or (b) small tubs that can be totally cleaned out frequently. Trying to steer a middle course (a new aquarium) is the riskiest method (although it can work OK). If you have a lot of eggs, it may be worth trying several methods to see what works best for you.