Operator and Analog: CLICK CLICK CLICK

[Stromkraft]

Why do you want to use Operator and Analog when you have Serum?

What kind of question is that??? What's wrong with Operator and/or Analog?

Clicky bass presets are usually caused by ADSR envelopes or phase mismatch. If you set the phase to retrigger for each note, it's wise to have the ADSR set in such a way that notes don't overlap or if they overlap then that the glide is enabled, which should override the retrigger. You can also have the phase free riding, so new note will start where the previous one left, but for certain types of bass lines this will make them 'swimming', i.e. even the same notes will not sound the same, especially in terms of punch / attack.

Analog sucks! Completely sucks. There are even better free plug-ins, like TyrellN6.
Operator is quite nice, but place it next to something like Serum and build similar patches and all you can do is cry and ask: why?

Of course, CPU concerns could be a valid reason to use Operator for some elements and the OP already explained the reasons.

[Stromkraft]

Try shortening the length of the midi notes

Because…?

if the notes are consecutive maybe the release is being abruptly cut off by the next note triggering. I'm not really sure
i just always leave a small gap between notes now and no clicks
sample with operator 1 sine voices changed to 1 no asdr adjusted
https://soundcloud.com/dubxile/sine-bass-click-sample
first loop gap between notes second loop notes begin and end on the grid

All you need to do in a proper synth is to adjust attack and release, and possibly check if retrigger is involved. There's seldom need to adjust note length. I'd rather drop Analog and Operator than mess with my musical expression. In fact, that's what I did. Good riddance.

[jujupython]

Same problem-resolved on Analog: Amp1 envelope any slope | check Legato |, master section - Glide |Check| any percentage.