Oh good. Yes. Let's please bring this up for the infinity-ith time. It is particularly relevent and useful to be mention when discussing an almost 40 year old letter. Thank you so much for making a useful contribution.
You're only losing opportunity cost. Not COGS. Meanwhile, the user who is pirating your software might be someone for whom the price is prohibitive or who would otherwise not be a user at all if there weren't a cracked alternative. So the the loss to this "theft" is actually much lower because (1) there was no price associated with materials for the software -- it costs you the same to produce one copy as it does a million and (2) the majority of cracked copies of the software wouldn't have resulted in a sale anyway.
(1) is debatable. The cost of living during development and the loss of potential savings count for price. If you estimate that as, say, 50k for a year-long project, then you need to do 50k of sales to break even on your investment. That shouldn't be a high number for a niche product that gets used, but I think it tends to be in software.
(2) I agree with. It doesn't matter what's best if your product doesn't sell. I think developers need publishing labels (read: app stores) to monetize. Users might pay not pay for note-keeping applet, but they might pay for a fork of it in their GitHub account that's been audited for security & privacy by a reputable publisher. Social P2P software can also be designed to exchange receipts of purchase on connection. Users would be able to disable it, but failing to publish a receipt for software would be awkward in business contexts.
Re: Your response to point (1). My statement stands. A development cost of $50k is a development cost of $50k regardless of how many copies are sold. Pirated copies do not cost the developer extra production expenses the way stolen physical merchandise would. If someone stole copies of Excel from a Best Buy, there would be costs associated with the packaging, DVD production, distribution, etc. that would need to be absorbed in order to replace the lost product. The only added cost per item online is the bandwidth cost, but that is absorbed by the person distributing cracked software rather than the original developer.
Keep in mind that the details surrounding copyrighting of software weren't solidified until the Copyright Act of 1976, which didn't go into law until 1978.
So at the time this letter was written, Micro-Soft's software didn't receive the automatic copyright protection we know of today.
I think he means it like stealing a credit card number opposed to stealing a car. The original owner still has the credit card number but the information has still been stolen.