If I come across a word in kana, but the dictionary says the word also has kanji, do I kanjify the word when I make a targeted sentence card for it?
Yes. When you make a card, convert the target word into kanji. Khatzumoto did it all the time, and it's practically a common thing among ajatters. I do it as well.
If you can read the kanji, then you can automatically read the kana. But if you can read the kana, it doesn't mean that you can read the kanji. By learning the kanji version you're getting both at the same time.
You could say that learning kanjified words is harder, but I don't see it as a big problem. Memorizing kanji readings is only difficult in the beginning. Plus, by learning kanjified words you create stronger memories.
If you already have a targeted sentence card that teaches the kanji version of a word, then the next time you make a card that has that word in it, you don't have to change it to kanji because it's not the target word anymore.
Most words in Ankidrone Starter Pack are kanjified for this reason.