You are close to my thinking. The issue isn't the number of shares so much as it is the total value of those shares.
As you say, the short term effect can be negative depending on what the company says it will use the money for.
As for your smaller ownership percentage argument, that depends on the size of the pie. A smaller slice of a larger pie can be more pie.
1 share at $5 = $5 .75 shares at $10 = $7.50
Anavex filed a shelf offering. Not a single share has been sold and the share price is getting pounded today. This S3 gave the shorts something to work with along with the mice PR, and they are making the most of it.