There are definitely some out there. Some might focus on their unique relationship dynamics, perhaps exploring how their different personalities interact. Others could be more adventure - based, with them going on quests together in the Homestuck universe. It really depends on what kind of story you're interested in.
Common themes include the struggle for understanding between them. Since they have distinct personalities, it can be a journey for them to truly understand each other. There's also the theme of loyalty. In the face of various challenges in the Homestuck universe, how loyal they are to each other can be a central theme. Additionally, some fanfics explore the theme of identity, as both characters have complex identities and seeing how they maintain or change their identities in relation to each other can be quite fascinating.
One popular plotline is a redemption arc for one of them through their interaction with the other. For instance, if Aranea has done some wrong deeds, Meenah might be the one to make her see the error of her ways. Another plotline could be them teaming up to outwit a more powerful adversary. They use their combined wits and skills to overcome the odds.
Well, in many Homestuck fanfics, Meenah and Aranea's relationship can be quite fascinating. Meenah's brash nature might clash with Aranea's more cerebral approach. For example, they could be in a situation where they have to work together despite their differences. This can create a lot of tension and drama in the story. Maybe they start off not liking each other but as the story progresses, they come to understand and respect one another in some ways.
You can try Archive of Our Own (AO3). It has a vast collection of fanfictions from various fandoms, including meenah x aranea ones. There are likely to be some great stories there.
One great meenah x aranea fanfiction is 'The Bond Beyond Worlds'. It beautifully explores their relationship's development. Another one could be 'Shared Secrets' which delves into their shared interests and how it brings them closer. There's also 'Unlikely Allies' that shows their journey from being strangers to something more.
You can try Archive of Our Own (AO3). It has a large collection of fanfiction from various fandoms, and there are bound to be some great Meenah x Karkat stories there. Just use the search function and type in their names.
One good one could be 'Meenah and Karkat's Unlikely Bond'. It shows how their different personalities, Meenah's brashness and Karkat's grumpiness, come together in an interesting friendship that might develop into something more. Another is 'Under the Sea with Meenah and Karkat' which takes place in a unique underwater setting and explores their relationship in that context.
A third common theme is cultural exchange. Naruto's world has its own unique culture with things like ninja villages, clans, and the way of the ninja. Aranea's world also has its distinct features. Fanfictions sometimes focus on how they introduce their respective cultures to each other and how they adapt to the new cultural elements.
A recurring theme is also that of discovery. They discover not only each other but also new aspects of themselves through their relationship. In many fanfictions, Noctis discovers his own strength and leadership qualities in a new light because of Aranea, and Aranea discovers a softer side to her tough - exterior because of Noctis. It's about how their relationship enriches their individual selves.