My fix for that is keep an instance of something like Plogue’s bidule in the rack (or optionally in a rewire instance, which can be advantage for a larger and more flexible bidule setup where one wants more control over processor thread assignment). I can then add/remove VSTi plugins in the bidule instance, and even tie in effect plugins from there and Cubase doesn’t glitch. With Bidule hosted as a plugin in Cubase, VST lanes show up in the DAW for hosted instruments, or can convert VST controls to/from MIDI based controls if needed/preferred…plus it provides OSC support that comes in handy if one wants to integrate some of that into a project as well (also possible to stage an instance of bidule stand alone combined with a virtual MIDI port and convert OSC into MIDI for a Cubase Generic Remote setup, as well as doing other advanced MIDI controller enhancement tricks before the signal hits a Cubase input).
For me it doesn’t matter most of the time…but there are cases where I know I’ll want to add/remove things while the project is playing with no glitch, and the bidule trick works for me. The work flow is something like…open a bidule instance that’s already in the Cubase rack. Have Bidule load whatever plugins I want and set them up before dragging it into the signal chain. While it’s often not necissary, one can take the precaution of setting up an A/B signal flow with a toggle or crossfader and get seamless A/B transitions across multiple signal chains, and such transitions can be automated from VST lanes, MIDI events, or OSC instructions if desired. Cubase has no idea we’re messing with things at this level, so it just keeps streaming along.
Bidule isn’t cheap (but less than a full version Cubase upgrade), and it’s not pretty to look at, but it’s very powerful/useful and has become a major swiss army knife sort of plugin that’s been well worth the investment. For both MIDI and Audio, it monitors, bridges, transforms, converts, modulates, records, plays, hosts, chains, supports multiple plugin types (VST2, VST3, AU) in the same instance, and bidule versions with discrete processing modes (threads independent of the audio clocks) also exist. Add an instance of the free ReaStream plugin, or set up jack2 on multiple rigs, and things can really get interesting if one wants to bridge plugins hosted on totally different machines over a LAN.