You may simplify them separately and merge them.
Given you have your 3 shapefiles in your folder, you could use a makefile a bit such :
#Merge:
final.json: map1.json map2.json world10m.json
topojson --id-property none --allow-empty -o final.json -- map1.json map2.json world10m_s.json
# Simplify:
world10m_s.json -- world10m.json
topojson --id-property none --allow-empty --simplify 0.5 -p name=Name -o world10m_s.json -- world10m.json
# SHP2JSON
world10m.json: world10m.shp
ogr2ogr -f GeoJSON world10m.json world10m.shp
map1.json: map1.shp
ogr2ogr -f GeoJSON map1.json map1.shp
map2.json: map2.shp
ogr2ogr -f GeoJSON map2.json map2.shp
Note: There are plenty of good reasons Why Use Make
Note2: Since topojson script also accept .shp for input, we could skip the #SHP2JSON task.