Ah, I was assuming you were still supplying the SD card with switched 3.3V via the PMOS pin. If you have it fed from the AMS1117, that regulator's internal overload protection would limit the inrush current into the capacitors, so there is nearly no risk of upstream port damage (till the AMS1117 dies from repeated abuse, and possibly shorts Vbus).
Ceramic capacitors have much lower ESR and self inductance than wound construction electrolytics, so are more effective for decoupling, especially at higher frequencies.
IMHO, you should order a selection of ceramic caps to hold in stock. Even free next day parts delivery from a good distributor, is no substitute for the convenience of only two minutes to select a cap from the box on the shelf.