Locusts might be plural, but 'thing' is the subject, and that is singular, so you should use is:
The only thing we haven't seen is locusts.
There must be subject-verb agreement. The subject is singular, so the verb form (in this case, is/are are forms of the verb to be) must match that.
Plural nouns, like 'locusts' can often be used as the generic plural to refer to that thing in general, or as a collected group.
Example:
- My favourite fruit is bananas.
- My biggest fear is spiders.
In these examples, 'bananas' and 'spiders' represent all bananas and spiders in general. It would be ridiculous to say "my favourite fruit is a banana" - it would sound like you have one special banana that you love. Likewise, in your example, 'locusts' means the insect in general, not any specific group of locusts, which is why they can be referred to as the singular 'thing' that has not been seen.
It is true that, sometimes, the verb can agree with the individuals of a group even when the group is the subject but normally only when both are named and only to emphasise the individuality of the group members. And of course, even native speakers make mistakes. So don't be misled by Google results that show the contrary. Google the phrase "the only thing is" and the erroneous "the only thing are", and you will get results for both - however, the first will get you 49,300,000 results, the first of which is a dictionary definition of the phrase; the second, wrong phrase, gets you 1,140,000 (less than 3% of the combined results) and the top results are two Stack Exchange ELL pages (one is yours) asking the question if the phrase is right or wrong. So anything but the usual subject-verb agreement you would expect to find is very uncommon indeed.