If we follow Twitter's rate limits of 450 requests per 15
minutes, will Twitter limit the number of queries we submit from our
API key?
No, Twitter will not limit you if you follow the rate limits. With Twitter4j, you could ask Twitter how many queries you have left.
Would it be possible to use GET search/tweets and obtain ALL
tweets and related data posted during 2016 that have the words Hillary
and Trump?
No, it won't be possible. As the documentation states:
The Search API is not complete index of all Tweets, but instead an index of recent Tweets. At the moment that index includes between 6-9 days of Tweets.
So, you can only get recent tweets from the search API. Be careful too with the data beacuse it's about relevance not completeness, from the same documentation:
Before getting involved, it’s important to know that the Search API is focused on relevance and not completeness. This means that some Tweets and users may be missing from search results. If you want to match for completeness you should consider using a Streaming API instead.
If you really need older tweets you will have to get them from other sources like Gnip (you need to pay). Otherwise you will have to approach differently your problem.
If you have the names (or id's) of all the users that you want to get info you could get the timelines from each user getting up to 3200 tweets.