You are right, Cell ends up using Solar Flare.
It is hard to get a definitive answer (because the question is pretty speculative), but I will argue that:
- Solar Flare has been shown to be incredibly disruptive every time it was used - in the manga, everyone affected by it was made helpless for at least ten seconds - having Trunks stop in mid-air because of it is not inconsistent with previous uses of that ability;
- I do not remember any character in Dragon Ball that could fight effectively while blinded, or without using his eyes - by implication, it means that there is nothing to suggest that ki sensing could replace eyes if someone was blinded. However, even if you find an example of someone that did fight without his eyes, you would still have to find something that Trunks would be capable of doing it;
The time that Cell took to absorb Android 18 was extremely short - I mean, if you look at the sequence depicted in the manga, it goes:
- Trunks blasts Vegeta to distract him;
- Trunks begins flying towards Cell, who is a few steps away from Android 18;
- Cell uses Solar Flare;
- Everyone is blinded;
- Cell gulps Android 18 down;
- The cloud generated by Trunks' blast around Vegeta dissipates;
I mean, damn, how long did it take Cell to absorb Android 18 after blinding everyone? 3 seconds? The disruption from Solar Flare clearly seems to be enough for this purpose.
However, I agree that the scene, as depicted in the anime, does not really make sense, as Android 18 and Krillin attempt to fight against Cell, while Trunks and Vegeta are completely forgotten about. It could be argued that they were affected more strongly because they were closer to Cell when he used Solar Flare, but that explanation seems dodgy.