In LGBC's case, I specifically opted NOT to have LibStub, CBH, AS3, LC, and AC3 as "no-lib", and while I did not hard embed any of them, I turned off the enabling of "no-lib" in LGBC's pkgmeta.
That way, end users who strip libs will only see one library (LGBC) instead of six. Well, five, as the Ace libs strip out as "Ace3" which contains the individual Ace libraries. Anyway, long story short, yes, I went with option 2.
Note that AceComm-3.0 MUST hard embed ChatThrottleLib due to its design. CTL is kind of not useful by and in of itself as a standalone library.
I will bet that Phanx might trample me like a horde of Horde, but you could look at LibGuildBankComm-1.0, which embeds AceComm-3.0 (which itself embeds ChatThrottleLib), AceSerializer-3.0, LibCompress, LibStub, and CallbackHandler-1.0.