Woocommerce – how to round up all prices to end in .99

You should try to use _regular_price meta key in your SQL query.

Regular price from the admin use the value of _regular_price key while the price shown at the frontend use the value of _price key. Keep in mind that _price is the active price of the product, if the product is currently on sale then the _price will use the value of _sale_price. The value of _price will be updated daily by default WC hook cron.