Normally in miniaturized equipment such as this, there is a dual-purpose input stage whose gain is controlled by the Mike/Line switch, followed by a stage whose gain is controlled by the record level knob. (The microphone and line-level inputs might be on separate sockets or they could be on a shared socket.)
Item #1 to consider--if you find that you can get close to 0 dB (full scale) levels by connecting your microphones to the line inputs--is that your microphones are evidently putting out relatively high signal levels, which might (depending on a whole host of variables) overload the input circuit of your recorder if you switched it over to "microphone."
However, if that's not the case--if you really have the luxury of a choice because both settings work without causing overload--then you reach item #2: There's likely to be some difference in the amount of preamp noise which gets recorded in the "line" setting versus the "mike" setting. But you have to make that comparison yourself on a case-by-case basis; the outcome isn't the same for all equipment. It's possible in some cases that a recording would have less noise in the mike setting, that it would have less noise in the line setting, or that there would be no audible difference in noise level between the two settings.
The equivalent noise of your recorder's input circuit is likely to be lower via "line in" than via "mike in," but if you choose the "line in" setting, you'll have to turn the gain knob up farther--and that may actually make everything noisier than it would have been if you'd used "mike in" with a much lower setting of the gain knob! And even if there might be a clear difference in a special quiet room, maybe the noise in any actual recording environment swamps the difference. It all depends.
If that seems like a non-answer, it's because the only way anyone can give you a more definite answer would be either (a) to use your recorder and microphones in the environments you typically record in, or (b) to go all the way over to the technical side and hash out all the specifications of your microphones and recorder--and then we'd still need an estimate of the maximum SPL and noise levels that occur in the recording venue.