It is important to understand that even when you configure a lambda function to be VPC enabled, the lambda functions don't actually run inside the customer's VPC. Lambda functions run inside a VPC and AWS account owned by the Lambda service team. The VPC enabled flag only allows lambda functions to connect to resources inside a customer's VPC. You can read up more about this here - https://docs.aws.amazon.com/lambda/latest/dg/configuration-vpc.html
So when a lambda function gets invoked by an SQS event source, SQS is not connecting to the lambda service using the customer's VPC. So you should be good.