How should I accommodate thinner replacement deck boards?
I would stay with 2 X lumber instead of 5/4 "decking". that will solve your dimension problem .  Regular 2 X lumber is twice as strong, twice as stiff and lasts much longer, compared to 5/4 decking. My deck is 2 X 6 , 25 years old and I have made a few repairs. The community pool has some 5/4 decking ,it has been replaced twice in that same time and does not look so good right now. More objectively ,the strength is proportional to the cube of the thickness; that cube is 3.38 for 2 X lumber and for 5/4 the cube is 1.95, so not quite 2 : 1 difference. Update- I went to the pool today ,5/ 23, a new deck had been put on during the winter ,so 3 decks in about 25 years. But, this time someone got smart and put in 2 X lumber instead of 5/4.