Sentence 1 is basically correct, although it needs commas to isolate the non-restrictive clause "which has many temples." Kyoto, which has many temples, is a nice city. As a matter of style, sentence 2 is generally preferable because new and heavy information usually goes at the end of the sentence. Here is an example: Example 1: [The direct and indirect objects are equally heavy. There is no preference for either version.] I gave [a present[ [to my mother]. I gave [my mother] [a present]. Example 2: [The direct and indirect objects are not equally heavy. The heavy direct object is preferred at the end.] I gave [an elegant black leather coat made in Italy] [to my mother]. I gave [my mother] [an elegant black leather coat made in Italy]. << preferred If you want more information, do a net search for "Definition and Examples of End Weight in Grammar." The article on the thoughtco dot com web site is meant for a general audience.

I agree with Chris. In #1, "which has many temples" is a parenthetical clause. That means that if you wanted, you could put it in parentheses: “Kyoto (which has many temples) is a nice city” The core of the sentence works very nicely without it: “Kyoto is a nice city”. Another way to handle #1 is to turn the parenthetical clause into an adjectival phrase to modify the subject of the sentence: “Having many temples, Kyoto is a nice city.” (The difference between a clause and a phrase is that a clause has a subject and a verb, whereas a phrase does not.)