Exactly Once Semantics means the processing framework such as flink can guarantee each incoming record(event) will be processed exactly one time even if the pineline fails in any way.
This is done by having checkpoints after each operation in the pineline, so that when the application recovers from failure, successful operation will not be executed again.
Depends on what kind of operations you are trying to do with databases, most cases databases are used as sinks for processing result to write into. In that case the operation involving database is just a simple insert and it will not be executed again after one successful run therefore it's still exactly-once regardless of its ACID support.
You might be tempted to group operations together for databases that support ACID but it will be a bad practice in a parallel streaming pineline since they created mutilple transactions and the locks might block the whole process. Instead, use BASE (NoSQL) database that are fast with intensive read and update performance is preferable, you just need to make your operations to be idempotent so that partially re-executed statements (if they failed half way through then after recovery they might be executed all again) won't result in incorrect data.