Have to wait or wait for it
“They had both noticed the looks of politely maintained blankness on their friends’ faces as they saw their apartment for the first time (the room with its two narrow twin beds—“Like something out of a Victorian asylum” was how Willem had described it to Jude—had gotten the most comments), but neither of them minded: it was theirs, and they had a two-year lease, and no one could take it away from them. Here, they would even be able to save a little money, and what did they need more space for, anyway?

Of course, they both craved beauty, but that would have to wait. Or rather, they would have to wait for it.”

_______Two options: one, "have to wait"; "have to wait for it". How to distinguish?
_____maybe useful information: later they become the couple.

Question

Have to wait or wait for it
“They had both noticed the looks of politely maintained blankness on their friends’ faces as they saw their apartment for the first time (the room with its two narrow twin beds—“Like something out of a Victorian asylum” was how Willem had described it to Jude—had gotten the most comments), but neither of them minded: it was theirs, and they had a two-year lease, and no one could take it away from them. Here, they would even be able to save a little money, and what did they need more space for, anyway?
 
Of course, they both craved beauty, but that would have to wait. Or rather, they would have to wait for it.”

_______Two options: one, "have to wait"; "have to wait for it". How to distinguish? 
_____maybe useful information: later they become the couple.

Answer

First, we have to find the subject and object of each sentence
1. that would have to wait--> Beauty would have to wait. (暂时美还不会来 （听起来好怪啊 但就是这么个意思啦 （美好的事物？
2. they would have to wait for it.--> the couple would have to wait for beauty. （他们得等美

So, to my knowledge, something that has to wait is something that cannot be done at the moment or that has to be set aside for awhile. （搁一边待会儿再做）(但你不知道到底谁把这东西放一旁待会做
ex. Success would have to wait.--> I don't have time or the ability to succeed right now, because I am too poor or I have to go to school right now.

The 2nd one is easier to understand, "to wait for something or someone". In this case, the couple is not trying to make beauty come, they do not do anything until the beauty comes. （很明确的是他们

Honestly, they mean the same thing. The only difference in this case is that there is a subject (they) in the second one, that is why it is easier to understand. That is why there is an "or rather" before "they would have to wait for it". The author wants to make it more clear by changing the sentence structure a bit.

还不懂的话用全中文解释也是可以的  :)

Answer

"They have to wait for it " is clear, no?
In their eagerness they remain in readiness for something to happen .Here 'wait' has this particular sense for they 'craved' beauty ,they couldn't afford it though obviously at that moment .

" That would have to wait "
This is a form of figurative language called 'personification '  ,giving human characters to inanimate objects or ideas even.
"Beauty has to wait " . It is used in literature and is considered an embellishing style ,that effects the imagination of the reader !

Answer

The phrases are two ways to say the same thing. The author is emphasizing by repetition.