I have an Amiga 1200 with an SD card and Classic WB installed. I have four drives DH0, DH1, DH2, DH3, when I start the machine with workbench it mounts all devices. If if start the machine using skip startup sequence then only DH0, DH1 and DH2 are mounted. How could I skip DH1 and DH2 from being auto mounted and how could I make DH3 be auto mounted?
Each partition on an Amiga hard drive has settings that determine whether it is bootable and whether it should be auto-mounted. It sounds like your DH3 partition is not set for auto-mounting, and the other 3 partitions are set for auto-mounting. Furthermore, you have a "Mount" command within your boot drive's S/Startup-Sequence that is causing DH3 to be mounted for a normal boot.
My recommendation would be to run HDToolBox from Workbench (probably in "Tools") to confirm the settings for auto-mounting on the 4 partitions. If you want, you can set only DH0 and DH3 to be auto-mount. Then, you could use Mount commands to mount DH1 and DH2 as needed.