"I thought 您 is more polite and honorific and thus should be used when address Jehovah. Why was "you" translated as "你" instead of "您"?"
你 is, in fact, the correct translation, not only linguistically; but theologically as well. Because God is Father, the familiar form of the second person is appropriate.
A little ...
In my opinion, this question is not specific in Chinese. In fact, many languages use the singular form of the second person to address God.
Here is a quote from Wikipedia's article "thou".
Early English translations of the Bible used the familiar singular form of the second person, which mirrors common usage trends in other languages. The familiar ...
From: Baidu: 您
“您”字并非属于通语字，这字原本为地方方言字-- The character “您” was not a standard character, it was originally a local dialect word
适用范围: -- Scope of application:
最初的方言字随普通话、通用书面传播到全国。-- The original dialect word spread throughout the country with Mandarin became standard writing.
Just to mention that in recent few years (from 2018 I'd say), it's increasingly popular to use TA (the pinyin letters of 他/她) to mean either 他 or 她, in casual or online writing. This is similar to the usage of s/he or him/her in English. For example
大声告诉TA (say it loudly to him/her)
Formally, 他 is still used to refer to a single person of unknown gender, but ...
In "心陪着你, 因为我想知道 她(他)是不是比我好"
He used '你'(you) to refer his ex-girlfriend at the beginning of the sentence. It is wrong to use a different pronoun "她" to refer his ex-girlfriend in the same sentence later.
她 has to be a typo, It should be '他' not ''她 in this line
"My heart is with you because I want to know if he is or isn't better ...