A word of warning on TinyCard user "Japanese Central"
If you've been over to the TinyCards site, I'm sure you've come across user "Japanese Central". Please avoid all of their decks. Each deck I've gone through has has numerous errors. Most of the errors seem to be including kanji on words that are usually in kana (animal names are huge offenders), including kanji on words that are supposed to be in kana (「こんにちは」 vs 「今日は」), to words that are flat out wrong (「乾酪」 vs 「チーズ」).
It seems like they found some nice-looking clip art and attached them to the worst selection of J-Dict reject translations. Please don't use them.
Most Japanese people would read 「今日は」 as 「きょうは」. That is, instead of reading it as "hello", they would read it as "as for today..." (e.g. 「今日は晴れです」).
Also, Jisho.org is horrible for learning Japanese. Anything using a J-Dict base will be unusable for learners, since it incorporates so many synonyms, slang usages, and other uncommon forms that it's practically unusable for the learner. If you're going to put a serious effort into learning Japanese, I highly recommend the Kodansha Furigana Dictionary or the Oxford Beginner's Japanese Dictionary.
I think instead of avoiding the card deck, it's ok to bring this matter to the maker's attention to correct any errors. As far as the examples you mentioned go, almost every Japanese word has a kanji: cheese can be written as チーズ and is also found in the dictionary as 乾酪, and こんにちは can be written as 今日は. Oh, and here's a fun fact: did you know that タバコcan also be written as 煙草? I've seen a tobacco shop with that sign during a trip to Nakasendo. It's just that for some words, their hiragana or katakana form became more common to use than their kanji.
I lived in Japan for awhile, and can definitely relate to the various words that can be spelled using kanji or kana. But the question is, what's best for someone learning? Are you going to teach 拉麺, considering that most of the time it will be written as ラーメン? Why confuse people like that?
I know that, as a beginner, I definitely appreciated being taught how things were usually done. Then, as I grew more confident, I could recognize the exceptions when I saw them. If I'd been taught all the exceptions as I was learning them, it'd have been far more difficult.
And as for 乾酪 vs チーズ... You don't get brownie points for using archaic/obscure words. If you were to say "thou donnest thy vestments" instead of "you put on your clothes", people would have a hard time understanding what you're saying. The best translation for cheese in modern Japanese is チーズ. Using anything else will only make people look at you weird.
Trust me, I completely understand what you mean, I’ve lived in Japan myself and would of course not write 拉面. But it is because I lived in Japan that I also know the Japanese concept (通じる）that means Japanese people WILL understand what the foreigner is trying to say or write, even if it sounds or seems strange.
I also do agree with you that nonetheless, proper Japanese language should be taught, and that the card deck should teach the more normal こんにちは rather than technically-correct-but-strange 今日は. I just think that instead of warning learners against the deck, giving feedback to the maker is a more positive action to take, and will do both the learners and the maker a favor, and improve their knowledge.