Perfboard is pretty meager stuff, but you can still try to help the signals: if it's the pad-per-hole kind, you can solder bare wire along pads as traces, and put ground traces either side of the signal trace. This makes a crude substitute for a "coplanar waveguide", which is a transmission line structure with useful impedance (in this case, probably around 100 ohms). Make sure to ground the ground traces at both ends, of course.
Just routing things with loose wires (the way perfboard is generally used), you get transmission lines through space with wild impedances (100-300 ohms?) and high coupling between them. The high impedance means these wires act like inductors (or even antennas -- if the switching edges are fast enough for the electrical length of the wires), which more readily puts bounce and crosstalk into your signals.
If you're literally just plopping down the OCXO to connect it to a transmission line, you won't have any other signals, and you'll have just one transmission line on a connector leaving the board. Keep that distance short and it won't matter. You may still want some resistance between squarewave output and connector, to help source terminate it (otherwise you have the hazard of reflections in the attached cable).
Tim