Yes, I'd say this rating is more or less accurate.
何 is usually read as なに・なん, and is one of the most basic words. Therefore, it's not a surprise for it to be N5.
方, read as かた or ほう, means a few things, but 日本の方、仕方、漢字の書き方, as you can see, are all pretty basic as well, 方法、正方形 are not too advanced either. Therefore N4.
どなた is basically a synonym of 誰, also one of the most basic words; therefore N5. There is also あなた and そなた, with the latter being somewhat archaic.
The problem with 何方{どなた} is not the word itself, but the spelling, namely the kanji. Yes both kanji and very basic, but this reading is not a normal reading, but a 熟字訓. Meaning it's got a special reading that's specifically for this kanji pair, and cannot be broken down to individual kanji. Like with 今日{きょう}, you can't separate 今 and 日, and it's not いまじつ, but when and only when this pair comes together, it's きょう.
So, while some words are simple, they're mostly spelled in ひらがな. The kanji version exists, but is not too common among Japanese people and therefore would be attributed a higher level. Other examples could be
- あなた・貴方{あなた}
- ここ・此処{ここ}
- いつ・何時{いつ}
There are some words whose kanji spelling are so rare most Japanese would not know of.
- かかし・案山子{かかし}
- さんしょううお・鯢{さんしょううお} but more commly 山椒魚{さんしょううお}
- そびえる・聳{そび}える
- えぐい・蘞{えぐ}い
- and way too many others to list exhaustively...
By themselves, かかし or さんしょううお or others are not necessarily hard words, but there kanji version is just too rare.
