As of my knowledge, there's no indication that Kaley Cuoco is pregnant on 'Based on a True Story'. Usually, such details would be reported in entertainment news if it were a significant part of the show, but I haven't come across any such news.
Well, indeed she was pregnant during that time. It's not uncommon in the entertainment industry for actors to be pregnant while filming. In Kaley Cuoco's case, during 'Based on a True Story', the production team had to make certain accommodations. For example, they might have used different camera angles or looser clothing for her character to hide the pregnancy if needed. And she was still able to deliver a great performance regardless of this situation.
Yes, some shows or movies she is in might be based on true stories. For example, if it's a biographical work about a real - life event or person that she portrays. However, without more specific information about which work of hers is being referred to, it's hard to be certain.