I also had the same issue so I went and tries to fix it. I managed to do this by finding the updated recipes from the space age expansion and added the categories to the assemblers/electronic assembler files manually. You need to add them to the bobs assemblers since they changed the categorie in space age, if you update bobs mods only with the new categories the EMP will work but the bobs machine lose access to these newly defined recipe categories.
NOTE; this has only been tested in my own run where I don't use any other bob's mods (only assemblers) So I can;t vouch for it being a good fix in any way shape or form and would recommend simply waiting on the update.
However if you are interested you can add the following lines to the following files in the mod folder:
Appdata/Roaming/Factorio/Mods/bobassembly.zip/bobassembly/data-updates.lua
data.raw.recipe["accumulator"].category = "electronics"
data.raw.recipe["discharge-defense-equipment"].category = "electronics"
data.raw.recipe["electronic-circuit"].category = "electronics"
data.raw.recipe["small-electric-pole"].category = "electronics"
data.raw.recipe["big-electric-pole"].category = "electronics"
data.raw.recipe["medium-electric-pole"].category = "electronics"
data.raw.recipe["copper-cable"].category = "electronics"
data.raw.recipe["advanced-circuit"].category = "electronics"
data.raw.recipe["processing-unit"].category = "electronics-with-fluid"
data.raw.recipe.substation.category = "electronics"
data.raw.recipe["plastic-bar"].category = "chemistry-or-cryogenics"
data.raw.recipe.explosives.category = "chemistry-or-cryogenics"
data.raw.recipe.battery.category = "chemistry-or-cryogenics"
Above adds all the new recipes in their new categories that were added/changed by space age.
Then in the assembly.lua and assembly-electronics.lua add these new categories to the crafting categories of each assembler type (or else the bob assemblers cant craft the changed recipes (ie green circuits) note that this will exapnd the available recipes in the electroics assembler (gives it everything in the eletronics category), but I don't care for that and this is just a temporary fix to the EMP problem until the mod is officially updated.
The lines for the crafting categories should look like this:
crafting_categories = { "basic-crafting", "crafting", "advanced-crafting", "crafting-with-fluid" , "electronics-with-fluid" , "electronics" },
do this for each assembler (they al have their own categories.
Also update the checmical plants (to prevent the same issues with changed categories for plastic)
checmical-plant.lua
crafting_categories = { "chemistry" , "chemistry-or-cryogenics" },