Does the sign matter for proportionality?

Mathematically they are equivalent, but physycist may want to differentiate between a force in the same direction as the displacement, and a force opposite to the displacement, as they lead to physically different behavior of the system. Thus the minus sign matters.

Yes, proportionality does not tell anything about the sign of the proportionality constant. This is probably done in physics so that the proportionality constant $k$ can be considered to be always positive. This has a physical interpretation , so it is convenient for it to be positive.