Yeah it sucks, but you'd have to decide if you want the escape pod more than the cargo you're carrying. You might be able to come back for it (if you can find it, of course). but I don't know how long ejected cargo hangs around for.
In context to the suggestion discussed here, we are talking about having a little bit of base cargo so you don't get locked out of rewards or gameplay because your ship build could not fit a cargo rack.
If you fill even that "safety space" before you go on a long trip and don't fit more cargo racks in your ship, then I guess you're the only one to blame.
But, you reply does highlight another issue with the suggestion of adding base cargo to all ships; players will find a way to use it that makes it's original intent useless. For instance, they may forget rewards in there and then complain it's not big enough to take more than one mission.