After a lot of research, I e-queried a well-known NY agent who has represented literary fiction that I feel is similar to mine. After several weeks, I had a very nice note from her assistant telling me how much she loved my first fifty pages and to please send a full. There was no mention of the agency owner, to whom my query had been addressed. I've sent it off and am continuing with my next novel and my queries on novel #1. Assuming--and this is a big assumption, I know--the assistant loves the full as much as the first fifty, what is likely to happen? I don't want to ask her directly at this point for fear of insulting her. Will the agency owner become involved? I looked up the assistant and she's listed on the agency website as actively seeking new clients (as is the owner). I can make certain assumptions about the owner based on her track record, but have no information on the assistant. She's young (no offense) and new to NY (after college). How can she possibly have the contacts the owner would have? Is it common for a response addressed to an owner to come from an assistant?
There are two main paths to becoming agent. The first is to work in a publishing house as an editor or a publicist for 20 years, burn out, and leave in a flurry of frustration about not being able to work with authors and having all of your projects crushed by upper management. The person takes all their contacts with them and becomes an agent, usually by joining a larger agency, and then breaking off when they have the client list to do so. This is the traditional way.
Today more and more people are jumping right from being assistants of agents to being sub-agents at that agency or a different one. I suspect the shift is largely because agencies are more likely to take on interns and assistants with no experience to help them get into publishing than a large, intimidating publishing company is, so more and more people start their careers at agencies (instead of publishing houses) and decide to stay.
If the assistant is listed as "taking on clients" for herself, then she is in the middle of making the transformation from assistant to sub-agent. Sub-agents get to use the name and resources of the head agent, which helps them get in doors and make contacts and have weight to throw around, but they also have to give a cut to the head agent. Eventually, they either build a client list strong enough to become a full agent (at that agency or elsewhere) or they don't and head into a different sector of publishing.
If the assistant is interested in being your agent, she's doing so with the tutelage of the head agent, so I wouldn't worry about it. She's also more likely to be agressively taking on clients because she needs to build a list to stay afloat financially if she's no longer being paid a salary like true assistants are.
I'm an assistant with no desire to move up the ladder because I don't actually want to be an agent. I don't particularly like working with contracts, bookkeeping, or publicity. I want to edit material, which is why I'll eventually end up in the editorial department of a publishing company, but I don't plan on making that jump until I finish graduate school.