When learning a trade one aspect will be quoting a job. It is a very interesting aspect and one that I think corresponds with the nursery industry.
As most of us are not able to complete a horticultural trade it would be great if we could get some insight from the professional nurserymen.
Professionals often have little tricks or formulas that makes amateurs, well look like amateurs

I imagine some of the things(overheads) you would have to take into account would be
Cost of growing area: Rent, mortgage, rates
Heavy machinery: Tractor, trucks or vans
Wages or time spent: Employees or self employed
Materials: Trees, seeds, soil, pots,wire
Consumables: water, fertiliser, various pest and fungicides,ware and tare on tools.
The idea would have to be something similar to finding the real cost of all these items over say one year and then work out what you would have to make to cover all these costs from he material produced.The other thing to consider is how much people are wiling to pay for what you produce. Due to the nature of Bonsai this may project over several years and cash flow would also need to be considered.
Now if we look at Japanese Bonsai nurseries as an example nurseries work in different stages.
From seedlings/cuttings to on growing and more refined specimens. These stages will overlap to some degree as well.
I imagine the early years of cultivation in bonsai could be worked out much the same as with standard nurseries, with some difference in how quality of the stock produced was evaluated.
I have found in Australia that the stock we buy from bonsai nurseries is often cheaper for the age of the stock than I can buy from a normal nursery. I figure the main influence here is that we buy direct from the producer. There is no middle man as such when you go to your local nursery who has to purchase from the initial grower.
Once we get to the growing on stage one thing we may have to consider differently is the extra time if any that each piece of material now needs. Time spent watering and other regular task such as fertilising and pest control may not change but it must be considered if more time is spent in styling consideration. One thing is certain it will need extra space so this will increase the cost of growing area over heads. Also another thing to be considered at this stage is payment for risk involved. The longer the investment goes for in the material the more chance your investment will collapse or at least a percentage of it. The proprietor must be compensated for risk. But at the same time it must be considered if people are wiling to compensate you for that risk (demand)
Onto the final stage and one thing here that also relates to the other stages but most evident here. Is the proprietor acting solely as a middle man or are they adding value to the material.
Most stages before this could be called craft. But now we delve into the more artistic side. I can't help but consider the difference between a domestic house painter and an artist that produces paintings we hang on our wall. Should one be paid more than the other for the time spent. I think not but there are some hidden considerations to take into account. A domestic house painter will have different over heads to an artist. The artists has time spent learning their trade to consider. Maybe there is years of study plus endless hours of research. The number of years of unpaid work to excel in their craft must be added to their overheads on any particular job. Also again we must consider payment for risk taken. An artist that spends many years learning their craft with the risk of failure must be compensated for that. Hence the better you become as an artist the more you are able to reap in reward.
In staying with this tangent we could consider a builder that is very good at renovating a house. The appeal of the final result will give the best returns.
Yet all the way through these stages one thing remains constant. The larger the operation the less each piece of material will cost which is in direct relation to overhead costs per piece of material.
Some believe that larger productions take away the artistic credit of bonsai but I disagree. I think that is heading in the direction of egotistical. They believe Bonsai is great because it is hard or difficult. They think that not everyone can do it. But I think bonsai is great no matter how easy it is.
In relation to this is Bonsai Nurseries such as Brussel's
http://www.youtube.com/watch?v=AmyRdflQu-g
People say this undermines bonsai but I think operations such as this, as they say, would be able to supply all level of bonsai quality at the lowest price simply because their overheads would be the lowest per specimen as they grow and buy then sell.
Other things that could be considered is has the material given any returns over the period of holding. IE in less professional gardens the enjoyment of having the material would have to be considered. Such that the re is not just a matter of producing income but is actually a joy to care for and improves ones enjoyment of life.
And in a more professional nursery the material may not be the bread winner but something to draw customers in. Similar in a way to a car dealer driving the latest model. (except that the material actually goes down in price the older it is

Little more to add but time for a break

