In formal writting in Chinese, should we write
Which one is considered more standard?
In formal writing in Chinese, should we write 事情已经过去了一万二千三百四十五天。
Only when you are writing in vertical writing format -- from top to bottom, right to left in columns
As for horizontal writing format like English, when we see sentence like "My phone number is 001-2000-110" we would read it as "my phone number is zero zero one- two zero zero zero- one one zero" but we would never write it that way. The same is true in Chinese if you write horizontally
As a Chinese, I would say that NO ONE CARES if you wrote "一万二千三百四十五" or "12,345".
The first one is written in Chinese numerals, the second one in Arabic numerals, they are much pretty the same.
If you insist on writing Chinese numerals, I would recommend you do say "事情已經過去了超過一萬天", if you want to emphasize that the event has passed for a long time.