You will have some of the same considerations of creating a mold when using wood as when using metal.
Underhangs/undercuts are to be avoided.
Corners are to be radiused, no sharp edges.
Alignment of mold halves must be ensured.
For your listed considerations, it doesn't appear that a wood mold, especially one made from hardwood would be a problem. With such a small item count, one can expect that you also do not need full automation. Manual processing of the bottle making will certainly save money.
Consider that you'll need someone to create the mold halves for you. If you have an existing positive model, it can be used to create the tool paths for a CNC router, although the size you've referenced would mean a router with a substantial thickness capacity. Hobby CNC routers are often limited to around 100 mm or so.
Finding someone to make the molds in wood will be your most challenging component.
Added below in response to comment:
Manual processing means opening the mold by hand, inserting the envelope of plastic, closing and clamping the mold and activating the injection of air. Placing the mold into a heated environment is also included in this sequence, as is removing it and de-molding the part.
This is to contrast an automated processing system where the mechanicals are constructed to be mostly hands-off. Push the button and everything happens at hundreds of parts per hour.
With respect to the type of wood, you'll likely have to experiment. Close-grained hardwoods will be strongest and most heat resistant as well. You'll have to test for heat based on the melting point or glass-transition temperature of your selected plastic. As with metal molding, pre-heat the mold prior to inserting the plastic, use appropriate safety gear.
Mold lifetime and other durability considerations will again depend on your selection of wood, as well as local availability of this material. As you've noted, you have CNC capability, which means a dozen molds aren't going to be much more expensive than one, in terms of material cost.