She thought ____ great honour to be invited to speak to us.

It and it was are both right.是两种不同的表达方法.It 是形式宾语,而后面的great honor 是实际宾语,后面的 to be invited to speak to us是宾补.
而it was great honor to ……是一个宾语从句做宾语.
它们是不同的结构,并不是系动词be的省略.而且,从语言习惯来说,显然She thought it great honor to be invited to speak to us更地道一些.

think it+名词/形容词+ to do sth.是个固定机构其中it是形式宾语,不定式to do sth.是真正的宾语,其中的名词或者形容词作宾语补足语。所以句中是it形式宾语,great honour 是宾语补足语,to be invited to speak to us是真正宾语。如果答案中把is改为was则thought后跟的是宾语从句因为主句用一般过去时态，所以从句也用过去时态。