No holes in PCB for BC548 Transistor?
Don't drill holes unless you want to mount the parts on the other side of board. You can use through-hole parts by cutting their leads short and soldering them end-on to the SMD pads.   

The SMD equivalent of a BC548 is BC848. Closest equivalent I can think of for the SK100 is BC807 (SMD version of BC327). It's only rated for 45V vs 50V, but this shouldn't be a problem unless your supply voltage is close to the limit. It's smaller power dissipation rating might be a problem, depending on how much current and voltage it has to handle simultaneously.   

I can't suggest an equivalent for the Zener diode because you haven't provided the part number for the through-hole version.