I grow my own chilis too also speciality types like habanero, congo black, white bullet, scotch bonnets etc (all in the hot hot hot range) and have also experienced the same change in yield for reasons I've never been clear on. My husband has a very high tolerance for spicy food and will eat a jar of pickled chilis (not peppers) in one sitting and cooks with birds eye/scotch bonnets varieties generally.
The Scoville scale is a measure of the hotness or piquancy of a chili pepper. These fruits of the Capsicum genus contain capsaicin, a chemical compound which stimulates chemoreceptor nerve endings in the skin, especially the mucous membranes. The number of Scoville heat units (SHU) indicates the amount of capsaicin present
The jalapeño rates between 2,500 and 10,000 Scoville units in heat. In comparison with other chili peppers, the jalapeño has a heat level that varies from mild to hot depending on cultivation and preparation. Most Scotch Bonnets have a heat rating of 150,000–325,000 Scoville Units.
But cultivation really has an effect, one year when I was very busy and forgot repeatedly to water a patio container of chilis to the extent the soil had drawn back from the container walls the chilis went nuclear in heat...
Absolutely lethal :-) and even reduced my husband to a coughing fit. So I figure there might be a relationship between available water and heat as well as quantity.
One year when Ive got the time Ill experiment further!
Fresh is the best, and I agree with Dagger that flavour is as important as heat although as stated above heat can be a little unpredictable. I'd use a milder chili and use more of it if necessary. Heat and flavour for me are better in fruits left to mature longer on the plant.
At the end of the day you know, chili, I reckon is a very personal thing :-) We select the fruits of the plants we like and carry on with those. Chili seeds propogate very well for us to the extent we no longer put them in our compost bin otherwise they turn up everywhere.
I always cook with seeds in, no de-veining.
P.S. Scoville references from wikipedia