Not at all too paranoid. Just like people figured out even with elastic everything, compute from Spot instances and all the other things we're supposed to do in AWS, the data out charges between AZ's and Region's still more than made up the cost savings for true resiliency. People are going to figure out relatively similar pricing traps in Cloudflare that are difficult to design around.
If you run an unindexed D1 query, then you get dinged for every row read. If you didn't properly perform scalability testing in non-production, then you'll never know this until you get a bill that you dissect to find out 5 million rows read for a 5 row result, if you even dig that far in the billing.
If you do not use the WebSocket Hibernation API with Durable Objects, then when you spin up a DO and hold open thousands of client WebSockets, you are being billed continuously for the entire time those connections are open—even if zero messages are being sent.
If you keep optimizing for payload size like many do by default but not event frequency (like poll a Worker every second instead of keeping a single stream open), it will show up unpleasantly in the billing.
If you treat KV like a transactional database keeping state, then be aware writes are expensive compared to reads. Pumping high-frequency write traffic into KV will result in exorbitant write operation costs and eventual consistency headaches. High-frequency state mutations belong in Durable Objects, not KV.
Batch your data to minimize request count, aggressively index your SQL queries to minimize row scans, and hibernate your idle persistent connections whenever you can. Doing all this will make your solutions cost efficient, but very locked into their ecosystem.