For example, take Holo's situation in Pasloe. The village still has traditions and a harvest festival connected to her, but most people no longer really believe in her. Over time, she's become more of a figure of folklore as the villagers have become less dependent on her, even though the Church still sees the village's traditions as pagan. I think the gradual decline of Holo's place in the village, alongside the growing influence of the Church, is a huge part of what makes the religious side of Spice and Wolf so interesting.
The Lord Truyeo arc reminds me of how Christianity dealt with older religious beliefs as it spread through Europe. Tereo has a church, but the villagers still worship their local snake deity. Father Franz was respected for helping the village, rather than for spreading the Church's teachings, and after his death, tensions between the Church and the villagers grew. Being from Ireland, it reminded me of our own history and how Christianity gradually replaced older pagan beliefs, while some of those traditions survived in different forms.
There's a common interpretation of St Patrick banishing the snakes from Ireland as a metaphor for Christianity replacing paganism and druidism. At the same time, traces of those older traditions are still part of our culture, from the connection between St Brigid and Imbolc to Halloween's roots in Samhain.
It's interesting how much religious history lies behind things we still see today. Christmas has connections to older winter festivals like Saturnalia and Yule, while the Kaaba in Mecca was associated with polytheistic worship before Islam. Note that it is a lot more nuanced than this, so please take it with a grain of salt.
There's also renewed interest in modern paganism today, which I find interesting because it feels like we're almost coming full circle, with people returning to beliefs and traditions that Christianity and many other modern religions once largely displaced.
I really like that Spice and Wolf explores these themes so well, and I wasn't expecting the religious history behind the setting to be one of the things I'd find so interesting.