My queen ant only laid 3 eggs. Is this bad?

Not necessarily. The first workers are often called nanitics because they are smaller than regular workers. This is turn is due to the queen rearing the ants from her own reserves. read more

The first eggs have to be cared for by the queen working by herself, so the first ants will be minims which are smaller than ants produced later in the colony’s life. If the eggs produce healthy ants you should be okay. read more

Another possibility is that the queen is actually eating the eggs and then lays new eggs (without you noticing it). This means that they would never develop into larvae. This can happen when the queen is stressed, for example when you tap the test tube often and/or when she is exposed to (bright) light. read more