I have a son (non-CF) that has a port. He has to have an IV infusion (10mL) 2x/week; so we use his regularly. The ONLY time we would leave him accessed is if we are using again in the next 24hrs. Otherwise we deaccess.
The concern you heard from the nurse was poorly worded; but valid. To explain I'm going to show you the 2 options to gain IV Access:
1) Peripheral (ie normal IV), meds go into a small vein, all you do is swab with Alcohol and go. It hurts, the vein doesn't hold up as well long-term as they are small and most IV drugs are caustic. However, they are quick and 'easy'.
2) Port, the meds go directly into the heart. Since anything happening at the port goes directly to the heart; you have to use sterile technique. Thus it takes a bit longer to do PROPERLY, and many (NOT ALL) hospital nurses frankly are not that good at it. Introducing an infection into the port can be very serious. However, a port lasts for years; you have less damage as the meds are introduced to a larger volume of blood, there is less pain to access as the skin above the port becomes 'tougher' over time.
That said, if you are comfortable with sterile technique, or trust your nurse, then don't be scared to un-access and restick later. Especially for showers/swimming/etc.
As for clotting, sorry but that is BS. There is always a risk of clotting, but done properly de-accessing doesn't change this risk (though it might actually reduce since you fill the port w/Heparin each time).