Hi,
The grammatically correct version is the sentence that doesn't end in a verb. "We investigate how strong the effect of X is on Y" is the best version. The formulation "We investigate how strong is the effect of XZY." is also grammatically correct because it doesn't end in a verb, preposition, etc. I would be more than happy to review your scientific paper. I have experience in editing proposals, grant requests, and lab assignments.
If you seek lessons, please feel free to message me.
Sincerely,
Starlyte