Generally your cheapest costs will be if all the parts are SMT and populated on a single side. Even if the parts cost somewhat more, the overall cost and handling may be worth it. If you can eliminate the heat sink by using copper area you may be able to save money and improve quality by eliminating assembly steps (for example, where an assembler could forget to put thermal grease on a part or insufficiently tighten a screw).
In smaller quantities (depending on where they are made too) it often makes sense to populate any through-hole parts manually after all the SMT parts are mounted.
These days often parts are only available in SMT, or the SMT parts are better than equivalent through-hole parts because of superior heat transfer through a thermal pad, say, but more often the SMT equivalents are inferior in mechanical robustness (especially things like connectors and switches), heat dissipation or some other characteristic.
For substituting things such as your TO-92 transistors, for example MMBT4401 is similar to 2N4401 but good for much less power dissipation. I would be very surprised if you cannot find a close equivalent or (more likely) a superior part for the TO-92 transistors.
Edit: You have mentioned a few part numbers in the below comment- 2N3904 and J310 JFET for example. There are no exact equivalents because the power dissipation and package is different, but MMBT3904 is likely the same die as the 2N3904 so it is very similar. MMBFJ310 is very similar to the J310 with small differences (eg. capacitance). In general, a capable engineer should review all substitutions including these ones, as well as any layout changes.
The 27N3LH5 power MOSFET is a more complex design question that would best involve looking at the entire application, but at a minimum would require estimating the power dissipation. In general you should review MOSFET part numbers from time to time as they are still improving and older parts are being obsoleted relatively frequently. Since the part you have has a rather high Rds(on) of 20m\$\Omega\$ you might be able to substitute a newer SMT part and greatly reduce the power dissipation and reduce the part cost. To do this does require at least the same knowledge and calculations as it took to originally design the circuit.