If we look at thee はまる, きこり, しじま and うつつ as three examples of many, they are spelt differently in different well known dictionaries.
はまる has 填まる first in Kenkyusha and Daijisen, while Meikyo and Shin Meikai have 嵌まる. The NINJAL-LWP from the corpus writes it with kana only.
きこり 樵 in Shin Meikai, Meiyo and Daijisen, but 樵夫 in Kenkyusha and 木こり in NINJAL.
しじま is kana only in Daijisen, Meikyo, Shin Meikai and NINJAL, but 黙 in Kenkyusha.
うつつ is kana only in NINJAL, 現 in Daijisen, Meikyo and Shin Meikai, but 現つ in Kenkyusha.
So my question is: is there any established, even if unofficial, standard to how these words should be written in a contemporary text? I'm asking both as a general question, but also because it would help me decide what spelling I should use in my flashcards. I see no point in learning what seem to be obscure spellings like 黙, but I also don't want to rely on Jishos "Usually written using kana alone", since I have already encountered loads of words that are very commonly written in kanji, that have such information.
I realize dictionaries have good reasons for their specific spellings. What I'm interested in is a good way to find out the preferable contemporary spelling of a word.