I also use deep litter method in my duck coop and have dug it out every 6 or so months. But I don't use straw, I use pine shavings. When I dig out, the bottom of the bedding is warm or even hot. That is great for keeping the ducks warm in winter. Not so desirable in NE Florida in the summer so I dig out around now when the nighttime lows are around 65F and rising. I haven't had your problem. I dig out the top layer of pine shavings [plus poo] on the parts of the garden where the ducks my trails. I also add the pine shavings from my brooder directly onto the duck trails. There is no appreciable smell. Digging out now onto the duck trails helps to control any mud as we move into our rainy season. The lower layers of bedding, which are black and composting in the duck house, go onto my compost pile. By the end of the summer, they are indistinguishable from soil, so in the fall, the compost pile gets dug out onto my vegetable beds.
After three years of doing otherwise, for the last 2 years I have had no food and water in the duck house [because I had a rat problem. After trapping the rats and banishing food and water, the rat problem resolved and I don't actually need to dig out every 6 months]. I add pine shavings on top of any poop every day and when there are wet pine shavings, I cover them with fresh dry shavings too. The smell of the pine shavings masks any smell from the poop very well. I used to periodically add a layer of oakleaves across the bedding in the duck house -- the leaves are readily available in March in much of the South. Since banishing food and water, I haven't needed to add a layer of oak leaves to start afresh with pine shavings on top.
So, my advice is to use pine shavings on top of your bedding now, to reduce the smell. And also change from straw to pine shavings for your deep layer litter. They are more absorbent of liquid poop than straw and also absorb mal-odors. I also think it's a good idea not to have duck food and water inside your duck house. Ducks are well able to go without food and water over night -- even in Winter when that might be for 12 hours