I have ordered a PCB for my circuit which includes transistor BC548 (Q1), SK100 (Q2) and a Zener diode (D2), but when I got the PCB it has no holes for those three components. Then I searched for SMD type equivalent of those, but their Pins are too distant as compared to my PCB.
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.