How to compute the number of ATP molecules that can be produced from breaking down an unsaturated free fatty acid?
Is the computation same and I just need to subtract a molecule of FADH2 per unsaturation (double bond)?

Definitely subtract a molecule of $\ce{FADH2}$. After all, you can skip the first of the the four steps in each cycle of removing two carbons (formation of double bond, adding water across the double bond, oxidizing the double bond to a carbonyl group, oxidative decarboxylation). You would also have to check whether any of the steps are coupled to ATP hydrolysis (e.g. the formation of the link to the acyl carrier protein, or transport steps) if you want to get an accurate number of ATP molecules synthesized per fatty acid turned into carbon dioxide.

The cis-isomer will be converted to trans-isomer completely skipping the step where the fatty acyl-CoA molecule is oxidized to the trans-form with the release of $\ce{FADH2}$.

Most unsaturated fatty acids in unprocessed food are in the cis-form. To turn them into the requisite $\ce{\Delta^2}$ trans-double bond, you need one or two additional enzymes, see https://www.ncbi.nlm.nih.gov/books/NBK22387/. For turning cis- into trans- and, if necessary, moving the double bond into the correct position, an isomerase is used. If there are two double bonds, one is reduced first by a reductase.