Back when the game was new, ProsciuttoMan put together a list of common misconceptions and ambiguous game concepts he saw players struggling with. I thought having a copy of that same list here might be helpful.

Truth: No, you don't. Beetle Ninja doesn't have a leveling system. Your stats are upgraded via in-game events that can be activated in the hub world. Fighting enemies only helps you to get a secondary currency that allows for the purchase of optional upgrades to your house.
Beetle Ninja himself is the only character capable of being upgraded, other ninjas are stagnant and their stats cannot be altered in any way.

Truth: Not at all. In fact, some missions are deliberately designed to be stealth-focused, forcing you to avoid enemies for the most part. You can still do so if you want to, it's just not how I'd do it personally.
The TL;DR of it is defeating enemies is only required when the game tells you it is.

Truth: You don't have one. The "D." counter is indicative of what day you're on in the game. It replaces the level counter because this is visible in the save screen, allowing players to easily gauge how far into the game they are.

Truth: There is no special ending for beating the game with Beetle Ninja alone, it's not something I planned on being possible whatsoever within the limitations I've set in place. I wouldn't recommend doing this personally.
If, however, I am sent video evidence of you beating the game's real ending with only Beetle Ninja, I will add a special ending just for you!

Truth: Though I wholeheartedly agree with the community's criticisms of Beetle Ninja, the game has gone far too under the radar for me to justify creating an enhanced version, knowing that the default version of the game hasn't captured people's interest.

Truth: The game is designed to be replayed, so there's certain things that are inevitably missable if you only play it once. Cash management and the hidden cats dictate that you can't really obtain all ninjas in a single playthrough, and the day skips are designed as a way to "payout" a day for some skill buffs.

Truth: You just have to beat 7 of the game's 11 missions. Going into it prepared isn't necessary, but I recommend having hired at least 3 ninjas throughout your playthrough.

Truth: I think it's ridiculous to think you should be able to play a game with the amount of content that Beetle Ninja has in your browser, so I think this complaint stems more from people who don't really play games very often. In short: RPGMaker 2003 doesn't export .html5 files, and thus it would be impossible to make it a browser game, even if I wanted to which I don't.