Does wiring a multi-cell battery pack to provide two different voltages adversely affect cell lifetimes?
The cells being used for both loads will be depleted faster than those being used for only one, at least if the lower voltage load is substantial in comparison to the higher voltage one.  If you then re-charge them in a charger not suitable for unbalanced starting conditions, this could be somewhat (to even seriously) detrimental, yes.

For chemistries with simple charging methods such as NiCd, NiMH, etc, simply using a low rate (1/10C) charger would probably not result in much of an overcharging problem for the less depleted cells - such chargers often have no timer or cutoff mechanism anyway (though they shouldn't be left connected constantly).  But a higher rate or peak-detect charger would not be appropriate.

For chemistries with more precise charging requirements, especially the various lithium cells, you would require a charger with a "balancing harness" - ie, an additional connector tapping out all of the internal cell terminals so that they can be individually charged and monitored to a safe level of charge.  It doesn't sound like you are talking about these types of cells, though.

If you have loose cells in a battery holder instead of a soldered pack, you could swap the doubly and singly used cells partway through the discharge cycle to partially equalize the usage.