The simple answer is yes.. and no.
Some - nearly all - manufacturers advise against hatching in your incubator (some even say if you do hatch in your incubator, it will void the warranty!) but they also advise on how to hatch in the incubator. Equally, a lot of experienced breeds say not to, while some say there is no better way than to hatch in the incubator. Clearly, Opinion on whether hatching in your incubator a good or bad idea is very divided.
And here's why. Hatching in your incubator can cause issues and stop the incubator from performing at its best. There is also the fact that you must clean your incubator thoroughly after each hatch or risk bacteria being left over from the previous hatch which could jeopardize the next hatch. It’s easier to use a separate hatcher as you don’t have to clean the incubator before you set more eggs. You'll also have 18 days to ensure your hatcher is clean before the next clutch are ready to hatch.
However, nearly all breeders - whether they be beginners, hobbyist or breeders - will hatch in their incubators and it is fine to do so.. if you look after the incubator. If you ensure that you keep up with the maintenance, you can hatch in your incubator without it doing any harm and the biggest - and arguably most important - task is cleaning your incubator.
After each hatch it is so important that you clean the incubator: removing all eggshell and hatching debris, cleaning the fans to ensure they are clear of chick down and disinfecting the incubator before your next hatch. If you do not remove the hatching debris and disinfect the incubator you could be exposing your next batch of eggs to bacteria that may cause harm to the embryo. It is also important to clean the fans and sensors. If the fans are clogged up with chick down, this can affect the air circulation and therefore the temperature. The same goes for the sensor or any other parts which are exposed like in the Rcom incubators; once covered in down, it can affect the accuracy of the reading.
One of the biggest things we see to cause incubators to fail - whether it be an old or new incubator - is them not being properly looked after. This includes not being stored in a cool and dry place, not being cleaned properly after each hatch and using tap, water instead of distilled or deionised water.