Yes you can import a 44.1 audio file into a project with a different sample rate. However, you will probably need to convert it to the project's sample rate.
In the Audio Bin you will find a menu command allowing you to convert the select file(s).
No need to worry about Software Instruments. They will be handled by Logic. Logic's internal bit depth is 32 bit floating point.
The best sample rate to run is a balancing act between perceivable quality and the end medium of distribution for your song.
e.g. If you are making music that will only be listened to on CD, then there is probably no point using a sample rate higher than 44.1. The higher the sample rate the less tracks, plugins etc your Mac will be able to process.
If your song will be used for film then 48 is the standard sample rate.
Most people will not be able to notice the difference in sound quality when you go above 48kHz...