In some ways, you are both right. The corrugated sheets do shade the plants in the greenhouse to a certain extent. Exactly how much would need to be measured with a light meter. It depends on various factors, such as the material and its thickness.
You cannot determine the effect of the additional cover on the plants with the naked eye alone. What seems bright to our eyes may not correspond to the plant's requirements in terms of amount of the light and the light spectrum. "Normal" thermal insulation glazing "swallows" about 30–40% of the light. A 16-mm polycarbonate double-wall sheet has a light transmission value (LT value) of almost 70%. So, if you cover one sheet with another sheet of the same type, only 70% of 70% of the light can get into the greenhouse, which is 49% of the light falling on the outer roof of the greenhouse. As such, it is certainly possible that with a double roof covering, relatively little light is reaching the tomatoes even if the eye cannot perceive the difference. Would it be possible for you to seal the damaged areas or replace the roof?
However, if the only result at this point is that you have fewer tomato flowers, you must keep in mind the early stage of the plant's life. At a height of 40 cm, you are really only just getting started. Or can you already see reduced growth across all the plants?
Just a word on keeping your greenhouse frost-free: Instead of using candles, you might find it easier to use a special greenhouse heater.