It's hard to answer this "generally"... there are many reasons to use kanji over hiragana, katakana over kanji, etc. But basically it's a stylistic choice. If you keep on reading manga, I think you will gradually understand the image of hiragana, katakana and kanji.
As for ひぐらしのなく頃に, なく seems to be intentionally in hiragana. Here's the official title logo:
なく is a verb which has many kanji with different meanings.
You should be able to distinguish 鳴く and 泣く because the difference is basic and important (see this page). The remaining two are poetic variants which are less important but have stronger rhetoric effects (typical 哭く is like this). So using hiragana なく will create ambiguity, and using the red color will make it look even more mysterious. The audience will wonder if there is some special meaning here.
As for 頃に, I doubt there is a special implication here. It is true that this 頃 should be written in hiragana in formal documents (because it's a 形式名詞), but novelists tend to ignore such rules and use whatever kanji they want. This 頃 looks fairly "normal" to me. If it had been in hiragana, all the letters in the title would have been in hiragana, which might give some other unwanted impression (being childish, too much "moe"-like, comedic, etc.).
