What does "y" really mean in Early Modern Spanish?

It is the same as AND:

Era la noche oscura, AND la hora las once; AND habiendo andado dos o tres calles AND viéndose solo AND que no tenía con quién hablar, determinó don Juan volverse a casa, AND poniéndolo en efecto, al pasar por una calle que tenía portales sustentados en mármoles, oyó que de una puerta le ceceaban. La oscuridad de la noche AND la que causaban los portales no le dejaban adivinar el ceceo. Detúvose un poco, estuvo atento AND vio entreabrirse una puerta. Llegóse a ella AND oyó una voz baja que dijo:

Y, as you first inferred, IS working as aa conjunction.

Regarding the redundancy, well, it is just preference of writing style. The writer preferred to use Y to CONJUNCT these sentences.

The same thing can be done in English:

The night was dark, AND it was eleven, AND having walked two or three streets, AND feeling himself alone AND that he had no one to talk to, he decided to go back home, AND doing so, while... (and so on and so forth)

And yes, as wimi pointed out, it can be used as aa literary device.

It was used in the past more often. Now, well, yes, indeed, it is used by writers that feel that Y gives their writing aa certain flavour.