I think you have run into a common misunderstanding here, and although I suspect you're searching for and finding the right docs, the incorrect context makes it all seem like nonsense or inapplicable.
So, you're actually looking at four different products and services here:
- h2 is a database that is providing the data storage for your Jira
- Tomcat is an application server (proper/explanatory name is "Apache Tomcat" or even "The Apache Foundation's Tomcat") - it is not a web server, it is a web-application server
- Jira is a web-application that uses a database (h2) to store data, runs on Tomcat, and throws up pages for users to interact with their data.
- Apache is a web-server (proper/explanatory name is "The Apache Foundation's Apache"), unlike Tomcat
So, you've mentioned three problems:
- speed (reported by humans)
- modern http protocols (reported by Jira)
- embedded database (reported by Jira)
The second and third can feed into the first, so let's get them fixed first.
The embedded database is simple - stop using h2 and swap to one of the supported databases (postgres, mysql, oracle or ms-sql). h2 is a file and memory based database which can run into performance issues quite quickly as it grows. More importantly, it can (and will) fail catastrophically. It should only be used for throwaway systems (development and testing), never one that you actually want to keep real data in. You should migrate as soon as possible.
The http protocols are a bit more complex to explain. There's a whole load of protocols that computers use to talk to each other, and some of them are insecure. Plain http is totally insecure and shouldn't be used for anything other than reading public information, but there are some https protocols that are no longer secure. Your Jira is using one of them.
This is where protocols get a bit more complex - we do not know how you have implemented it. By default a Jira install uses http, but it's not actually the Jira (or database) that does https, and you should always use https for Jira access. You can do it in the Tomcat, or you can stick your Tomcat behind a proxy that does the https for you, and that's where the Apache web-server kicks in.
The a2en/a2dis commands you've mentioned are for the Apache web-server, not Tomcat.
So, two actions
1. Let us know how you are doing https (if at all! If it is https, is it just Tomcat, or have you got a proxy of some form?)
2. Migrate to a supported database
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