Back when I bought my SE, it was cheaper than getting a 6, despite having better specs. I also check for deals online a lot, and the SE was almost constantly being discounted. I think it's not unreasonable, based on these, to assume that it never really sold particularly well.
Based on that, I'd say that they stopped making the SE simply because only a very small, specific slice of the market actually wants to purchase such a device, and it's not worth keeping a unique product in their portfolio if the sales numbers just aren't there.
Five percent of iPhones is still an enormous number when Apple sells ~200,000,000 iPhones per year. (And that's despite Apple not catering for this market for the past three product cycles. Imagine if they did!)
Based on that, I'd say that they stopped making the SE simply because only a very small, specific slice of the market actually wants to purchase such a device, and it's not worth keeping a unique product in their portfolio if the sales numbers just aren't there.