DISCLAIMER: This is not legal advice. No reader should act or refrain from acting based on what is said below. Each reader should consult an attorney as each situation is different, and what is said below may not be applicable.
We typically see this handled as such. The Plan will have a section entitled "Stock Subject to the Plan," and the opening sentence will read, "The maximum aggregate number of Shares that may be issued under the Plan is 1,00,000 Shares, all of which Shares may be issued under the Plan pursuant to Incentive Stock Options."
In that same provision, there will then be language that says - "Notwithstanding the foregoing, subject to the provisions of Section [X] below, in no event shall the maximum aggregate number of Shares that may be issued under the Plan pursuant to Incentive Stock Options exceed the number set forth in the first sentence of this Section plus, to the extent allowable under Section 422 of the Code and the Treasury Regulations promulgated there under."
We do not typically advise clients to add a percentage, nor do we see when we're asked to review Plans on behalf of an employee or consultant, a Plan that lists only a percentage of the shares subject to the Plan can be classified as ISOs.
And yes, each amendment to the Plan should include a review of the number of shares included in the Plan and any other stipulations that may need to be included as part of the amendment.
A lot could be discussed when dealing with ISO compliance, but hopefully, this answer helps as additional food for thought as you discuss it with others.