Why are only some of the references censored in Lucky Star
Not sure if this is just a random connection or actually the reason, but here's the connection between Lucky Star and ToHeart:

Lucky Star's manga and anime are published by different branches of Kadokawa. The ToHeart manga was published by MediaWorks which was owned by, you guessed it, Kadokawa.

I don't know if every single branch of Kadokawa is allowed to mention a work in every other branch, but there is at least this connection. If someone bought Lucky Star DVDs and saw ToHeart mentioned and then decided to go buy the ToHeart manga, that's a double win for Kadokawa.