In either case, you probably want to upgrade. Even 5.005 is "old",
so the upgrade to 5.6.1 is probably advisable.
Correct. R 1.6 will unconditionally assume 5.005.
1.4.1 instead. Can I expect this to cause any problems, for
instance when I build a package?
Possibly, though probably only Kurt et al could say for sure.
As Fritz said: yes, but I'd recommend upgrading Perl to 5.005 or even
5.6.1.
Unfortunately, that is not an option at the moment. I guess most
people working with R are professionals with the means to work
with relative new hardware. I have to make do with a very old
system, a disk drive that is almost full, so no possibility to
compile a recent version of gcc, or upgrade anything that
demands a C compiler that is not from last century.
I write quite some software myself. Working with an old system
like I have has the advantage that I never hear people complain
that my software doesn't work on their system because there
system is too old.