Lot of assumption. If Dany gets pregnant, it does not necessarily mean it's only because they're both Targaryens.
There is a practical reason for the Targaryen practices of incest, as it ensures their bloodline continues to be able to ride dragons.
Targaryens have been married to other houses. Aemon's brother King Aegon V was married to Betha Blackwood(Riverlands House, blood of the First Men). Others have married with House Martell(Rhaegar and previous Targs), houses with Valyrian roots, House Dayne etc.
The purity reason is just monarchy bs, just like historical monarchs in the real world.
I know the practical reason about bloodline and being able to command dragons and such. I had the impression that Daeny would think about a future where that didn't matter too much due to her generally progressive notions about a better world within Westeros.
I'm kind of worried because the show seems to be hammering home the point that Daeny seemingly can't conceive children several times this season. It also made official, even with heavy handed implications in the past, that Jon is also partial Targaryen. Then they have sex to end this season.
If Daeny reveals that she's become pregnant next season, and the only reason the show can point to is "oh it's because she slept with another Targaryen!," despite the greater lore acknowleding Targaryen compatibility with a wide range of other houses/humans, I feel like it heavy-handedly validates racial purity, on the backs of what were seeming to be relatively progressive-leaned characters.
I also understand and get the political drama that might come about from Jon learning of his Targaryen heritage, and I'm okay with that aspect, but if Daeny is able to conceive a child with Jon and seemingly no one else and the only proof is because he's got Targaryen blood, then I think that's a really lame creative choice.
They seem to constantly chalk up how much more powerful Daeny was as a Targaryen compared to some of her more direct ancestors, too, and this season finale had the explanation given about how small and weak the dragons had become due to the various forms of corruption her more direct ancestors had adhered to, and lent it to the reason for their weakness. If the strongest Targaryen in a long time is suddenly also only compatible to procreate with another Targaryen, it's literally fantasy saying "the strongest could only create more strong children with another of its own ilk," which I feel kinda flies in the face of all the isle of misfits fighting for their place in the world theme that I get from Daeny and her team.
EDIT:
Dany got pregnant through Drogon remember lol? Something happened in that tent when the witch was performing the black magic thing. Also, Rhaegar had two children with Ellia Martell, and the Martells were brought into the kingdom due to marriage pacts. They can have children with other people easily. The Targaryens practiced incest for Dragon controlling purposes more likely.
Dany's bit with the non pregnancies were more likely some BS that witch put into her head as Jon pointed out.
yes, I hope so...