Since there is no way to tell neutrinos and antineutrinos apart
There is. Neutrinos are distinguished from antineutrinos since they have opposite signed lepton number and opposite chirality relative to each other. They were also first detected in 1956 as part of an experiment to first detect neutrinos.
does conservation of lepton number make any sense?
Yes. Conservation of lepton occurs in beta decay for example. In beta decay
$$n \rightarrow p^{+} + e^{-} + \bar \nu$$
or
$$p^{+} \rightarrow n + e^{+} + \nu$$
where in the first reaction, lepton number before = 0 and after +1 + (-1) and for the second reaction, 0 = -1 + (+1). Clearly conservation of lepton number is followed (and the same for all other interactions involving neutrinos and antineutrinos) and does indeed make sense.
lepton number is not a conserved quantity?
Yes, it most certainly is.