Hum, yes. If you're not using VPC endpoints, basically you're routing all your AWS traffic to the open internet.
Not only is it wasteful and slow, but that also means you have to open free lunch internet egress on your instances, or implement some convoluted DNS based firewalling.
Using VPC endpoints also allows you to capture AWS service traffic and apply policy on it, such as whitelisting which buckets are accessible, thus avoiding internal data leaks.
Honestly there is just no argument for _not_ using VPC endpoints. Even on a purely architectural point of view, having you AWS traffic being routed out to internet just to get back in makes no sense.
If you are still unconvinced, the pricing argument of course still stands.