I faced sentence with word order that is different from expected "我们两个是好朋友" instead of "我们是两个好朋友". Does it have some different meaning?
Not much of a different depends on the question asked if this is an answer:
我们两个是好朋友 - Us two are good friends 我们是两个好朋友 - We are two good friends
As Ben Yang pointed out, 我们是两个好朋友 is not quite idiomatic. It's because 两个好朋友 (two good friends) is not a unity. You can say 我们是一对好姐妹；我们是一对夫妻，where 一对好姐妹 or 一对夫妻 is a unity.
我们两个是好朋友 is idiomatic, meaning we two are good friends.