So you’re thinking something, but you are uncertain, and then it’s confirmed and you want to say that you guessed it. In such situations, people often say “C’est ce que je pensais” (“That’s what I thought”) or “Je m’en doutais” (“I suspected as much”) or similar things.
“Je l’aurais pensé/cru” has this connotation of something that is false but that you would have been unsurprised to learn was true, mostly because it’s conditional as opposed to the above’s past. It would in fact almost always have that meaning. As an example:
Ah, ils ne forment pas un couple? Je l’aurais pourtant cru!
As a complement to Kareen’s answer, you could also use:
Je le savais (I knew it)
J’en étais sûr (I was sure about it)
Je l’aurais parié !